Methods to spatially profile protease activity in tissue and sections

ABSTRACT

Aspects of the disclosure relate to methods and compositions useful for in vivo and/or in vitro enzyme profiling. In some embodiments, the disclosure provides methods of in vivo enzymatic processing of exogenous molecules followed by detection of signature molecules as representative of the presence of active enzymes associated with diseases or conditions. In some embodiments, the disclosure provides compositions and in vitro methods for localization of enzymatic activity in a tissue sample.

RELATED APPLICATIONS

This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application Ser. No. 62/483,245, filed Apr. 7, 2017, the contents of which are incorporated herein by reference in its entirety for all purposes.

FIELD

The disclosure relates, in some aspects, to improved methods and products associated with detecting, localizing, and monitoring the activity of proteases in vivo or in vitro. These methods and products form the basis of, and may be used as, an ultrasensitive diagnostic platform.

BACKGROUND

Early detection of tumors offers the hope of greatly improved outcomes for cancer patients. For the majority of cancer types, diagnosis when the disease is localized to the organ of origin correlates with significantly greater long-term survival compared with when the disease has spread to distant sites, largely because currently available therapeutics are most effective when patients are treated in the early stages of disease. Despite the need for technology that can detect early-stage disease, the predictive value of existing biomarkers used to diagnose cancers is limited. For example, researchers have observed that screening with the blood biomarker CA-125 for ovarian cancer diagnosis does not improve patient prognosis. However, screening with biomarkers that are predictive can significantly improve patient outcomes: colorectal cancer (CRC) mortality at 30-year follow-up was reduced by 32% with annual fecal occult-blood testing.

Despite the progress in improving tumor detection tools, clinical detection of tumors is limited to masses ˜1 cm in diameter via imaging techniques (for example, magnetic resonance imaging (MRI) and positron emission tomography) and analysis of blood biomarkers shed by the tumor (for example, proteins and cell-free nucleic acids). It is estimated that it can take up to ten years to establish tumors this size from the initial tumorigenesis, leaving a large window of opportunity for early diagnosis to improve patient outcomes.

SUMMARY

Aspects of the disclosure relate to the surprising discovery that pro-diagnostic reagents comprising certain modifications (e.g., surface presentation of enzyme susceptible domains, functionalization with a tumor-penetrating ligand, or a combination thereof) are capable of improved in situ localization of enzymatic activity in tissue samples. In some aspects, the disclosure relates to the surprising discovery that pro-diagnostic reagents described herein are capable of detecting tumors (e.g., enzymatic activity associated with a tumor) having a size less than 1 cm in diameter, which is below the limit of detection of previously utilized activity-based monitoring molecules, in vivo.

Accordingly, in some aspects, the disclosure provides a pro-diagnostic reagent comprising: (a) a carrier domain linked to a signature producing domain, wherein the signature producing domain comprises an enzyme susceptible domain linked to a signature molecule, wherein the enzyme susceptible domain is susceptible to cleavage by a disease-associated enzyme, and, (b) one or more tumor-penetrating ligands, wherein each tumor-penetrating ligand is linked to the carrier domain.

In some embodiments, a carrier domain is greater than 5 nm in size. In some embodiments, a carrier domain is smaller than 5 nm in size.

In some embodiments, a carrier domain is a nanoparticle, RGD peptide, protein, polymer, aptamer, or antibody. In some embodiments, a carrier domain is an iron-oxide nanoparticle.

In some embodiments, a carrier domain is linked to the signature producing domain by a linker molecule. In some embodiments, a linker molecule comprises one or more poly(ethylene glycol) (PEG) molecules. In some embodiments, a linker molecule comprises between 2 and 200 PEG molecules.

In some embodiments, an enzyme susceptible domain is susceptible to cleavage by an enzyme associated with cancer, tissue injury or damage, cardiovascular disease, arthritis, viral, bacterial, parasitic or fungal infection, Alzheimer's disease emphysema, thrombosis, hemophilia, stroke, organ dysfunction, any inflammatory condition, vascular disease, parenchymal disease, or a pharmacologically-induced state.

In some embodiments, a disease-associated enzyme is a serine protease, matrix metalloprotease (MMP), thrombin, kallikrein, matriptase, hepsin, cathepsin, plasminogen activator, or ADAM.

In some embodiments, a signature molecule is a peptide, nucleic acid, small molecule, fluorophore (e.g., a fluorophore, or a fluorophore/quencher pair, such as a FRET pair), carbohydrate, particle, radiolabel, MRI-active compound, ligand encoded reporter, or isotope coded reporter molecule (iCORE).

In some embodiments, a signature molecule comprises a fluorescence resonance energy transfer (FRET) pair. In some embodiments, a FRET pair comprises a fluorophore molecule and a quenching molecule. In some embodiments the fluorophore molecule and the quenching molecule of a FRET pair flank an enzyme susceptible domain of a pro-diagnostic reagent as described by the disclosure. In some embodiments, a quenching molecule is proximal to a carrier domain relative to a fluorophore molecule. In some embodiments, a fluorophore molecule is proximal to a carrier domain relative to a quencher molecule. In some embodiments, a FRET pair is 5-Carboxyfluorescein (5-FAM) and CPQ2.

In some embodiments, a signature molecule is a fluorophore. In some embodiments, a signature molecule is an iCORE. In some embodiments, a signature molecule is cyanine7 (Cy7).

In some embodiments, a tumor-penetrating ligand is a peptide, polypeptide (e.g., antibody), polymer, aptamer, or small molecule. In some embodiments, a tumor-penetrating ligand specifically binds to a p32 receptor, neuropilin-1 (NRP1) receptor, αvβ3 integrin receptor, αvβ5 integrin receptor, folate receptor, transferrin receptor, Her2 receptor, or EGFR. In some embodiments, a tumor-penetrating ligand is LyP-1 (CGNKRTRGC; SEQ ID NO: 1) or iRGD (CRGDKGPDC; SEQ ID NO: 2).

In some embodiments, a tumor-penetrating ligands is linked to a carrier domain by a linker molecule. In some embodiments, a linker molecule comprises one or more poly(ethylene glycol) (PEG) molecules. In some embodiments, a linker molecule comprises between 2 and 200 PEG molecules.

In some embodiments, a carrier domain comprises a plurality of enzyme susceptible domains, a plurality of ligands capable of binding to the tissue sample, or a combination thereof.

In some aspects, the disclosure provides a method for determining the location of disease-associated enzyme activity in a tissue sample, the method comprising: (a) contacting a tissue sample obtained from a subject with a pro-diagnostic reagent, wherein the pro-diagnostic reagent comprises: (i) a carrier domain linked to a signature producing domain, wherein the signature producing domain comprises an enzyme susceptible domain linked to a signature molecule, wherein the enzyme susceptible domain is susceptible to cleavage by a disease-associated enzyme, and, (ii) one or more ligands capable of binding to the tissue sample, wherein each ligand is linked to the carrier domain; wherein the one or more ligands bind the carrier domain to the biological sample prior to cleavage of the enzyme susceptible domain by the disease-associated enzyme; and, (b) subjecting the tissue sample to an analysis method in order to detect the presence of the signature molecule, wherein the presence of the signature molecule in the tissue sample is indicative of the location of disease-associated enzymatic activity within the tissue sample.

In some embodiments, a subject is a mammal, such as a human. In some embodiments, a tissue sample is a flash-frozen tissue sample. In some embodiments, a tissue sample is obtained from the brain, lymph node, breast, liver, pancreas, colon, liver, lung, blood, skin, ovary, prostate, kidney, or bladder of a subject. In some embodiments, a tissue sample comprises cancer cells.

In some embodiments, an analysis method is a multiplex analysis method. In some embodiments, an analysis method involves mass spectrometry (such as liquid chromatography-mass spectrometry), PCR analysis, DNA microarray, fluorescence analysis, or ELISA. In some embodiments, an analysis method is a singular analysis method.

In some aspects, the disclosure provides a method for detecting a tumor in a subject, the method comprising (i) administering to a subject a pro-diagnostic reagent, wherein the pro-diagnostic reagent comprises (a) a carrier domain linked to a signature producing domain, wherein the signature producing domain comprises an enzyme susceptible domain linked to a signature molecule, wherein the enzyme susceptible domain is susceptible to cleavage by a cancer-associated enzyme, and, (b) one or more tumor-penetrating ligands, wherein each tumor-penetrating ligand is linked to the carrier domain; (ii) subjecting a biological sample obtained from the subject to an analysis method in order to detect the presence of the signature molecule, wherein the presence of the signature molecule in the biological sample is indicative of the subject having a tumor.

In some embodiments of methods described herein, a pro-diagnostic reagent is administered to a subject via a systemic modality, such as intravenous injection.

In some embodiments, a tumor detected by a method described by the disclosure is less than about 1 cm in diameter. In some embodiments, a tumor detected by a method described by the disclosure is between about 1 mm and about 5 mm in diameter.

In some embodiments, a biological sample is a urine sample or a blood sample. In some embodiments, the signature molecule is cleaved form the enzyme susceptible domain at a site that is remote from the biological sample.

BRIEF DESCRIPTION OF DRAWINGS

FIGS. 1A-1F show MMP9 is upregulated across human cancers. FIG. 1A shows analysis of fold change in MMP9 mRNA expression in tumors versus healthy controls; compiled from Oncomine and TCGA data. H&N, head and neck; Mela, melanoma; OV, ovarian; GBM, glioblastoma multiforme; COAD, colorectal adenocarcinoma. FIG. 1B shows ROC curves constructed on the basis of MMP9 mRNA expression data to represent how well MMP9 can classify various cancer types versus healthy controls (median AUC=0.81). FIGS. 1C and 1D show immunohistochemical staining of MMP9 protein in normal (Norm) and ovarian carcinoma from a human TMA (FIG. 1C) and corresponding staining scores for tumor (n=20 cores) versus normal (n=5 cores) tissue (FIG. 1D). Blinded analysis of staining was performed by a pathologist; 3 for the highest level of staining and 0 for no visible staining. FIGS. 1E and 1F show immunohistochemical staining of MMP9 protein in normal colon and COAD from a TMA (FIG. 1E) and corresponding expression scores (FIG. 1F). Full TMA staining is shown in FIG. 2D.

FIGS. 2A-2E show TCGA mRNA and human tissue microarray analysis of MMP9 expression. FIG. 2A shows mRNA expression of MMP9 is elevated in breast cancer samples compared to normal adjacent tissue based on analysis from The Cancer Genome Atlas. FIG. 2B shows MMP9 mRNA is elevated across all stages of breast cancer compared to normal adjacent tissue based on analysis. FIG. 2C shows scoring of MMP9 staining in tumor and normal tissue from ovarian, breast, lung, and prostate. Cores were scored by a pathologist in a blind manner. FIG. 2D shows a scan of tumor microarray stained with MMP9 antibody. Tumor microarray was purchased from US BioMax, Inc. (Catalog No. MC5003b). FIG. 2E shows several MMPs showed significantly upregulated expression across breast cancer stages compared to normal adjacent tissue (Two-tail Student's t test for a; 1way ANOVA with Dunnet's posttest for FIG. 2B & FIG. 2E; *P<0.05, **P<0.01, ***P<0.001; n=22 for normal, 39 for Stage I, 42 for Stage Ia, 9 for Stage Ib, 26 for Stage II, 164 for Stage IIa, 103 for Stage IIb, 10 for Stage III, 65 for Stage IIIa, 13 for Stage IIIb, 19 for Stage IIIc, 13 for Stage IV, 9 for Stage X).

FIGS. 3A-3K show in vitro and in vivo experiments and in silico evaluation for engineering of a tuned ABN. FIG. 3A shows a schematic depicting FRET-based protease substrate displayed on an ABN surface. The sequence corresponds to SEQ ID NO: 22. FIG. 3B and FIG. 3C show cleavage velocity (V) of an MMP9 substrate by MMP9 (FIG. 3B) or thrombin (FIG. 3C) for 0, 4, 24 and 114 PEG subunits. Lines represent the fit to the Michaelis-Menten equation (mean±s.e.m., n=2-3). FIG. 3D shows the ratio of MMP9 and thrombin velocities at a substrate concentration of 6 μM (RFU, relative fluorescence units). FIGS. 3E-3G show accumulation of LyP-1 ABNs and NTP ABNs (controls) in excised tumors (FIG. 3E) and quantification of ABN signal in tumors (FIG. 3F) and organs (FIG. 3G); mean±s.e.m, n=7 for NTP ABNs and n=8 for Lyp-1 ABNs. FIG. 3H shows a schematic of parameters varied in a mathematical pharmacokinetic model. FIG. 3I and FIG. 3J show change in detection signal when optimized parameters (BC, background cleavage; TC, tumoral cleavage; TA, tumoral accumulation) were applied to 10-mm (FIG. 3I) versus 5-mm (FIG. 3J) tumors (light shading denotes additional signal gained when parameters are combined, compared with BC+TC+TA). FIG. 3K shows kinetic traces of the detected urine signal (tumor−control) with all three parameters optimized (left line), and the contribution to the signal of increasing the TA term (right line).

FIG. 4 shows thrombin cleavage of thrombin substrate varies on surface presentation. A thrombin substrate was presented on the nanoparticle surface with varying linker lengths (n=2-3, ±SEM). Unlike the MMP substrate, an intermediate length was optimal for thrombin catalysis. Data was fit to the Michaelis-Menten equation. The sequence corresponds to SEQ ID NO: 23).

FIGS. 5A-5C show characterization of targeted vs untargeted nanoparticles. FIG. 5A shows spectra of LyP-1 and non-tumor penetrating (NTP) ABN. Iron oxide absorbs at wavelengths shorter than 400 nm, LyP-1 is tagged with 5FAM dye, the nanoparticle core is labeled with VT-680 and the peptide substrate is labeled with Cy7. FIG. 5B shows peptide substrate valencies were matched between the two nanoparticles. FIG. 5C shows physicochemical characterization of particles by dynamic light scattering shows a hydrodynamic diameter of 60.11 nm and a surface potential of −3.82 mV.

FIGS. 6A-6E show tuned ABNs detect sub-5 mm diameter tumors. FIG. 6A shows a schematic depicting urine testing in a mouse flank tumor (MDA-MB-435 xenograft) model; i.v., intravenous. Study time course for urine testing is also shown. FIG. 6B and FIG. 6C show relative reporter concentrations in the urine normalized to urine signal in healthy mice after administration of NTP ABNs (FIG. 6B; mean tumor size for 50+ bin, 146 mm³) and LyP-1 ABNs (FIG. 6C; mean tumor size for 50+ bin, 132 mm³). Tumors from seven (NTP ABNs) or eight (LyP-1 ABNs) mice measured over three weeks were binned by tumor size; mean±s.e.m., two-tailed Student's t-test, *P<0.05, **P<0.01; ρ is the Spearman correlation between urine signal and tumor size in individual mice. FIG. 6D and FIG. 6E show ROC curves and calculated AUC values for NTP ABNs (control; FIG. 6D) and LyP-1 ABNs (FIG. 6E).

FIGS. 7A-7B show half-life measurements of ABN and free reporter. FIG. 7A shows blood half-lives of LyP-1 and non-penetrating particles are matched (data fit to one-phase exponential decay). FIG. 7B shows kinetic measurement of the free reporter in the blood and urine after intravenous injection.

FIGS. 8A-8E show growth characteristics and urine signals of MDA-MB-435 flank xenograft. FIG. 8A shows caliper measurements of tumor sizes across both groups were consistent, reaching 100 mm³ total burden by week 3. FIG. 8B shows a histogram of tumor sizes for urine data binning. FIG. 8C shows photographs of flank tumors in nude mice. Targeted synthetic biomarkers were able to classify tumors at week 2. Volumes reported are calculated after measurements performed using a digital caliper. Urine signal for mice administered (FIG. 8D) non-penetrating ABNs and (FIG. 8E) LyP-1 ABNs over time course of the study (P-value represented on each graph as calculated by repeated measures ANOVA) are also shown.

FIGS. 9A-9G show urinary biomarkers outperform blood biomarkers in detecting millimeter-sized lesions in orthotopic xenograft models of ovarian cancer. FIG. 9A shows a schematic of LyP-1 ABN testing in an ovarian cancer model. FIG. 9B shows immunohistochemical staining of excised tumors (scale bars, 100 μm). FIG. 9C shows size distribution of tumor nodules retrieved from the intraperitoneal space of a representative animal at two weeks after tumor initiation. Average total tumor burden at this time point was 36 mm³. FIG. 9D and FIG. 9E show accumulation of ABNs in tumor nodules in a representative animal (FIG. 9D; scale bar, 1 cm) and biodistribution of ABNs in organs (FIG. 9E; mean±s.e.m, n=10). FIG. 9F shows urinary measurements of ABNs (bars) and blood measurements of HE4 (black line); mean±s.e.m, n=10 per group, two-tailed Student's t-test, ***P<0.001). FIG. 9G shows a ROC curve of urinary diagnostic and blood biomarker.

FIGS. 10A-10F show HE4 secretion rates across several ovarian cancer lines. FIG. 10A shows a standard curve for the HE4 ELISA. FIG. 10B shows secreted HE4 across several lines was measured by collecting supernatants. Data is normalized to get secretion rate per million cells per day. FIG. 10C shows cytoplasmic HE4 was measured by collecting and lysing cells. OVCAR-8 cells have relatively high secretion and cytoplasmic HE4 compared to cells profiled. FIG. 10D shows cleavage of MMP9 substrate by conditioned media collected from OVCAR-8 cells with and without the MMP inhibitor, Marimistat. Marimistat can inhibit a significant portion of the cleavage. FIG. 10E shows correlation of tumor volumes as measured by imaging of retrieved nodules after necropsy versus bioluminescence imaging. FIG. 10F shows bioluminescence imaging shows that on average, tumor burden increases over time.

FIGS. 11A-11G show urinary biomarker performance in the ovarian cancer model. FIG. 11A shows a plot of LyP-1 ABN accumulation, as measured by fluorescence intensity, and tumor diameter from the 10 mice shown in FIG. 9F. Linear regression shows that total nanoparticle accumulation was correlated with size of individual tumor nodules (Pearson's r=0.767). FIG. 11B shows total tumor burden was measured at the time when detection became statistically significant for blood biomarker (n=10, 3 weeks; HE4) or for the urinary biomarker (n=10, 2 weeks). The limit of detection for LyP-1 ABN was at a tumor volume of 36 mm³ while the limit of detection for blood biomarker HE4 was at a tumor volume of 88 mm³. FIG. 11C shows distribution of nodule diameters recovered from each mouse at time of positive detection (n=10 each group). FIG. 11D shows tumor and non-tumor mice were imaged live (top), then sacrificed and the abdominal cavities opened to image tumors without skin attenuation (middle). Visible tumors were resected and mice were imaged again (bottom). FIG. 11E shows luminescence from tumor bearing mice before and after tumor resection was measured, and it was calculated that 17.4% and 17.8% of tumor signal was remaining, respectively. FIG. 11F shows resected tissue is luminescent, suggesting that mostly tumor cells were removed. FIG. 11G shows cell standard OVCAR-8 cells was also imaged, with a limit of detection below 3,000 cells.

FIGS. 12A-12G show minimally invasive receptor classification of syngeneic liver metastasis via targeted ABNs. FIG. 12A shows LyP-1 and iRGD both engage the same tumor trafficking pathway but rely on different primary receptors. LyP-1 and iRGD ABNs were tested in a liver metastasis model. The sequences correspond to LyP-1 (CGNKRTRGC; SEQ ID NO: 1) and iRGD (CRGDKGPDC; SEQ ID NO: 2). FIG. 12B shows a MRI image of a CLM mouse with 40 mm3 of total tumor burden; tumor nodules are indicated by arrows. FIG. 12C shows Haemotoxylin and Eosin staining (scale bar, 5 mm) and immunohistochemical staining of tumor sections for the primary receptors, p32 and αv integrin, and the secondary receptor, NRP-1 (scale bar, 200 μm). FIG. 12D shows imaging of tumor center and margin, as well as normal liver, in sections from CLM mice. The tumor margin is indicated by a dashed line and the inset is indicated by a box. Sections were stained for nuclei and MMP9; scale bar, 100 μm. FIG. 12E shows bioluminescence imaging of CLM mice over time (mean±s.e.m, n=20). ABNs were administered when luminescence readings reached 107 photons s-1 cm-2 sr-1. FIG. 12F shows fluorescent scans of tumors showing ABN accumulation (left scale bar, 2 cm; right scale bars, 5 mm) and line traces of ABN and liver autofluorescence (in relative fluorescence units) corresponding to the dashed lines. FIG. 12G shows relative reporter concentrations measured in the urine of healthy mice versus CLM mice after application of LyP-1 ABNs (n=10 mice) or iRGD ABNs (n=9 mice); the mean±s.e.m is denoted by a horizontal line with error bars; two-tailed Student's t-test, ***P<0.001.

FIGS. 13A-13C show MC26 cell line surface marker analysis by flow cytometry. FIG. 13A shows MC26 cells in culture express integrins. FIG. 13B shows MC26 cells in culture express Neuropilin-1. FIG. 13C shows that MC26 cells in culture do not express p32. Traces indicating IgG control for each sample are also shown.

FIGS. 14A-14B show iRGD ABNz characterization. FIG. 14A shows absorbance spectra of iRGD ABNz. Spectra matches LyP-1 ABNz, except iRGD does not have a FAM label. FIG. 14B shows mouse MMP9 is readily able to cleave the selected MMP9 substrate.

FIGS. 15A-15D show clearance of ABN in vivo. BALB/c mice were injected with iRGD ABN intravenously and fluorescence was measured in (FIG. 15A) blood and (FIG. 15B) urine every 24 hours for 7 days. FIG. 15C shows organs were collected 3 hours, 24 hours, and 7 days after ABN administration and fluorescence was measured compared to a PBS injected control. Reporter signal in the blood, urine, and organs was undetectable at 7 days (n=3, + SEM for all time points). FIG. 15D shows nude mice bearing orthotopic ovarian tumors and injected with ABN have similar urine clearance kinetics with no detectable signal after 1 day (n=5, ±SEM).

FIG. 16 shows toxicity screening of ABN. Immunocompetent BALB/c mice were injected with iRGD ABN, and organs (heart, lung, liver, spleen, and kidney) were collected at 3 hours, 24 hours, and 7 days after administration. Organs were fixed, embedded in paraffin, and stained with hematoxylin & eosin. Analysis by a veterinary pathologist confirmed that tissue from ABN injected animals appeared similar to PBS injected control. Study was done with n=3 mice and images from a representative animal are shown. Scale bar represents 100 μm.

FIG. 17 shows correlation between MRI computed tumor volume and bioluminescence. MRI and bioluminescence measurements were made by two separate, blinded operators (r: Pearson's correlation).

FIGS. 18A-18C show imaging of nanosensor localization. FIG. 18A shows biodistribution of LyP-1 or iRGD targeted nanoparticles. FIG. 18B shows a fluorescent scan of livers with tumor metastases administered iRGD or LyP-1 targeted synthetic biomarkers or uninjected controls. Scale bar indicates 2 cm. Uninjected controls show no nanoparticle fluorescence. Tumors are not autofluorescent (arrow). FIG. 18C shows photographs of excised livers. Tumors are delineated by lack of autofluorescence.

FIGS. 19A-19B show performance of targeted nanosensors in liver metastasis model. FIG. 19A shows iRGD targeted sensors can differentiate liver metastasis bearing mice from age-matched mice that received a sham surgery (n=5 per condition; ±SEM; Student's t-test, two-tailed, *P<0.05). FIG. 19B shows a plot of an individual mouse relative urinary signal against tumor luminescence. Tumor luminescence between iRGD and LyP-1 groups were similar.

FIGS. 20A-20E show ABN zymography is responsive to human tissues. FIG. 20A shows a schematic of ABNs re-engineered for zymography (ABNz). Nanoparticles were modified with iRGD targeting ligands and FRET-pair flanked substrates that increase their fluorescence on proteolytic cleavage. Frozen sections of CLM livers collected from mice were bound with PBS only (−ABNz), ABNz without divalent cations necessary for iRGD binding, and ABNz. Tissues were subsequently cleaved in MMP9 buffer with and without MMP9 inhibitor and imaged for the bound ABNz (ABNzb) and cleaved ABNz (ABNzact); scale bars, 50 μm. FIG. 20B shows application of iRGD ABNz to a human CRC tumor microarray consisting of 20 colorectal adenocarcinoma (COAD) samples and 20 normal adjacent tissue (NAT) (scale bar, 2 mm). FIG. 20C shows extent of signal co-localization between COAD and NAT samples scored on a scale of 0 to 3 by a blinded independent researcher. FIG. 20D shows a higher-magnification image of the boxed area in FIG. 20B showing a patient sample containing cancer (left) and normal adjacent tissue (right); scale bar, 400 μm. FIG. 20E shows magnified tissue from boxed area in FIG. 20D showing cell-level co-localization of activated ABNz with integrin and MMP9 staining (scale bar, 40 μm).

DETAILED DESCRIPTION

Current approaches to measure protease activity in tissue sections rely on measuring cleavage of fluorescently labelled protein gels overlaid on the tissue. Other approaches involve directly binding active proteases, either using antibodies that bind the active site of the protease of interest or activity-based probes that covalently bind to active proteases, for example as disclosed in WO2014/0255313. The evaluation of substrate cleavage in tissue sections using the approaches mentioned above presents several challenges. For example, substrate typically diffuses away from the location of the active protease. Furthermore, currently available activity-based probes are typically unable to detect tumors that are less than 1 cm in diameter.

The compositions and methods of the disclosure have a number of advantages over the prior art methods. For example, compositions and methods described by the disclosure are useful, in some embodiments, for localizing enzyme substrate to a tissue prior to proteolysis, as opposed to enabling tissue binding after proteolysis, and then measuring protease activity on the substrate (e.g. measuring enzymatic activity in situ on a tissue sample). In another example, pro-diagnostic reagents comprising one or more ligands that bind to a tissue (e.g., tumor-penetrating ligands) greatly increase the sensitivity of pro-diagnostic reagents described by the disclosure, thus making them capable of detecting tumors that are less than 5 mm in diameter.

Accordingly, in some aspects, the disclosure provides a pro-diagnostic reagent comprising: (a) a carrier domain linked to a signature producing domain, wherein the signature producing domain comprises an enzyme susceptible domain linked to a signature molecule, wherein the enzyme susceptible domain is susceptible to cleavage by a disease-associated enzyme, and, (b) one or more tumor-penetrating ligands, wherein each tumor-penetrating ligand is linked to the carrier domain.

Carrier Domain

A pro-diagnostic reagent as described by the disclosure typically comprises a modular structure having a carrier domain linked to an enzyme susceptible detectable marker. As used herein, the pro-diagnostic agent is non-natural (i.e., synthetic). A modular structure, as used herein, refers to a molecule having multiple domains.

The carrier domain may include a single type of enzyme susceptible detectable marker, such as, a single type of enzyme susceptible domain and/or detectable marker or it may include multiple type of enzyme susceptible detectable markers, such as, different enzyme susceptible domains and detectable markers. For instance each carrier may include one type of enzyme susceptible detectable marker or it may include 2-1,000 different enzyme susceptible detectable markers or any integer therebetween. Alternatively each carrier may include greater than 1,000 enzyme susceptible detectable markers. Multiple copies of the pro-diagnostic reagent are administered to the subject. Some mixtures of pro-diagnostic reagents may include enzyme susceptible detectable markers that are enzymes, others may be enzymatic susceptible domains, and other may be mixtures of the two. Additionally a plurality of different pro-diagnostic reagents may be administered to the subject to determine whether multiple enzymes and/or substrates are present. In that instance, the plurality of different pro-diagnostic reagents includes a plurality of detectable markers, such that each enzyme susceptible domain is associated with a particular detectable marker or molecules.

The carrier domain may serve as the core of the nanoparticle. A purpose of the carrier domain is to serve as a platform for the enzyme susceptible detectable marker. As such, the carrier can be any material or size as long as it can serve as a carrier or platform. Preferably the material is non-immunogenic, i.e. does not provoke an immune response in the body of the subject to which it will be administered. Another purpose is that it may function as a targeting means to target the modular structure to a tissue, cell or molecule. In some embodiments the carrier domain is a particle. A particle, for example, a nanoparticle, may, for instance, result in passive targeting to tumors by circulation. Other types of carriers, include, for instance, compounds that cause active targeting to tissue, cells or molecules. Examples of carriers include, but are not limited to, microparticles, nanoparticles, aptamers, peptides (RGD, iRGD, LyP-1, CREKA, etc.), proteins, nucleic acids, polysaccharides, polymers, antibodies or antibody fragments (e.g., herceptin, cetuximab, panitumumab, etc.) and small molecules (e.g., erlotinib, gefitinib, sorafenib, etc.).

As used herein the term “particle” includes nanoparticles as well as microparticles. Nanoparticles are defined as particles of less than 1.0 μm in diameter. A preparation of nanoparticles includes particles having an average particle size of less than 1.0 μm in diameter. Microparticles are particles of greater than 1.0 μm in diameter but less than 1 mm. A preparation of microparticles includes particles having an average particle size of greater than 1.0 μm in diameter. The microparticles may therefore have a diameter of at least 5, at least 10, at least 25, at least 50, or at least 75 microns, including sizes in ranges of 5-10 microns, 5-15 microns, 5-20 microns, 5-30 microns, 5-40 microns, or 5-50 microns. A composition of particles may have heterogeneous size distributions ranging from 10 nm to mm sizes. In some embodiments the diameter is about 5 nm to about 500 nm. In other embodiments, the diameter is about 100 nm to about 200 nm. In other embodiment, the diameter is about 10 nm to about 100 nm.

The particles may be composed of a variety of materials including iron, ceramic, metallic, natural polymer materials (including lipids, sugars, chitosan, hyaluronic acid, etc.), synthetic polymer materials (including poly-lactide-coglycolide, poly-glycerol sebacate, etc.), and non-polymer materials, or combinations thereof.

The particles may be composed in whole or in part of polymers or non-polymer materials. Non-polymer materials, for example, may be employed in the preparation of the particles. Exemplary materials include alumina, calcium carbonate, calcium sulfate, calcium phosphosilicate, sodium phosphate, calcium aluminate, calcium phosphate, hydroxyapatite, tricalcium phosphate, dicalcium phosphate, tricalcium phosphate, tetracalcium phosphate, amorphous calcium phosphate, octacalcium phosphate, and silicates. In certain embodiments the particles may comprise a calcium salt such as calcium carbonate, a zirconium salt such as zirconium dioxide, a zinc salt such as zinc oxide, a magnesium salt such as magnesium silicate, a silicon salt such as silicon dioxide or a titanium salt such as titanium oxide or titanium dioxide.

A number of biodegradable and non-biodegradable biocompatible polymers are known in the field of polymeric biomaterials, controlled drug release and tissue engineering (see, for example, U.S. Pat. Nos. 6,123,727; 5,804,178; 5,770,417; 5,736,372; 5,716,404 to Vacanti; U.S. Pat. Nos. 6,095,148; 5,837,752 to Shastri; U.S. Pat. No. 5,902,599 to Anseth; U.S. Pat. Nos. 5,696,175; 5,514,378; 5,512,600 to Mikos; U.S. Pat. No. 5,399,665 to Barrera; U.S. Pat. No. 5,019,379 to Domb; U.S. Pat. No. 5,010,167 to Ron; U.S. Pat. No. 4,946,929 to d′Amore; and U.S. Pat. Nos. 4,806,621; 4,638,045 to Kohn; see also Langer, Acc. Chem. Res. 33:94, 2000; Langer, J. Control Release 62:7, 1999; and Uhrich et al., Chem. Rev. 99:3181, 1999; all of which are incorporated herein by reference).

Polymers include, but are not limited to: polyamides, polycarbonates, polyalkylenes, polyalkylene glycols, polyalkylene oxides, polyalkylene terepthalates, polyvinyl alcohols, polyvinyl ethers, polyvinyl esters, polyvinyl halides, polyglycolides, polysiloxanes, polyurethanes and copolymers thereof, alkyl cellulose, hydroxyalkyl celluloses, cellulose ethers, cellulose esters, nitro celluloses, polymers of acrylic and methacrylic esters, methyl cellulose, ethyl cellulose, hydroxypropyl cellulose, hydroxy-propyl methyl cellulose, hydroxybutyl methyl cellulose, cellulose acetate, cellulose propionate, cellulose acetate butyrate, cellulose acetate phthalate, carboxylethyl cellulose, cellulose triacetate, cellulose sulphate sodium salt, poly(methyl methacrylate), poly(ethylmethacrylate), poly(butylmethacrylate), poly(isobutylmethacrylate), poly(hexylmethacrylate), poly(isodecylmethacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), poly(octadecyl acrylate), polyethylene, polypropylene poly(ethylene glycol), poly(ethylene oxide), poly(ethylene terephthalate), poly(vinyl alcohols), poly(vinyl acetate, poly vinyl chloride and polystyrene.

Examples of non-biodegradable polymers include ethylene vinyl acetate, poly(meth) acrylic acid, polyamides, copolymers and mixtures thereof.

Examples of biodegradable polymers include synthetic polymers such as polymers of lactic acid and glycolic acid, polyanhydrides, poly(ortho)esters, polyurethanes, poly(butic acid), poly(valeric acid), poly(caprolactone), poly(hydroxybutyrate), poly(lactide-co-glycolide) and poly(lactide-co-caprolactone), and natural polymers such as alginate and other polysaccharides including dextran and cellulose, collagen, chemical derivatives thereof (substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), albumin and other hydrophilic proteins, zein and other prolamines and hydrophobic proteins, copolymers and mixtures thereof. In general, these materials degrade either by enzymatic hydrolysis or exposure to water in vivo, by surface or bulk erosion. The foregoing materials may be used alone, as physical mixtures (blends), or as co-polymers. In some embodiments the polymers are polyesters, polyanhydrides, polystyrenes, polylactic acid, polyglycolic acid, and copolymers of lactic and glycoloic acid and blends thereof.

PVP is a non-ionogenic, hydrophilic polymer having a mean molecular weight ranging from approximately 10,000 to 700,000 and the chemical formula (C₆H₉NO)[n]. PVP is also known as poly[1-(2-oxo-1-pyrrolidinyl)ethylene], Povidone™, Polyvidone™, RP 143™, Kollidon™, Peregal ST™, Periston™, Plasdone™, Plasmosan™, Protagent™, Subtosan™ and Vinisil™. PVP is non-toxic, highly hygroscopic and readily dissolves in water or organic solvents.

Polyethylene glycol (PEG), also known as poly(oxyethylene) glycol, is a condensation polymer of ethylene oxide and water having the general chemical formula HO(CH₂CH₂O)[n]H.

Polyvinyl alcohol (PVA) is a polymer prepared from polyvinyl acetates by replacement of the acetate groups with hydroxyl groups and has the formula (CH₂CHOH)[n]. Most polyvinyl alcohols are soluble in water.

PEG, PVA and PVP are commercially available from chemical suppliers such as the Sigma Chemical Company (St. Louis, Mo.).

In certain embodiments the particles may comprise poly(lactic-co-glycolic acid) (PLGA).

The carrier may be composed of inorganic materials. Inorganic materials include, for instance, magnetic materials, conductive materials, and semiconductor materials.

In addition to particles the carrier may be composed of any organic carrier, including biological and living carriers such as cells, viruses, bacteria, as well as any non-living organic carriers, or any composition enabling exposure of enzyme substrates to enzymes in disease (including extracellular, membrane-bound, and intracellular enzymes).

In some embodiments, the particles are porous. A porous particle can be a particle having one or more channels that extend from its outer surface into the core of the particle. In some embodiments, the channel may extend through the particle such that its ends are both located at the surface of the particle. These channels are typically formed during synthesis of the particle by inclusion followed by removal of a channel forming reagent in the particle.

The size of the pores may depend upon the size of the particle. In certain embodiments, the pores have a diameter of less than 15 microns, less than 10 microns, less than 7.5 microns, less than 5 microns, less than 2.5 microns, less than 1 micron, less than 0.5 microns, or less than 0.1 microns. The degree of porosity in porous particles may range from greater than 0 to less than 100% of the particle volume. The degree of porosity may be less than 1%, less than 5%, less than 10%, less than 15%, less than 20%, less than 25%, less than 30%, less than 35%, less than 40%, less than 45%, or less than 50%. The degree of porosity can be determined in a number of ways. For example, the degree of porosity can be determined based on the synthesis protocol of the carriers (e.g., based on the volume of the aqueous solution or other channel-forming reagent) or by microscopic inspection of the carriers post-synthesis.

The plurality of particles may be homogeneous for one or more parameters or characteristics. A plurality that is homogeneous for a given parameter, in some instances, means that particles within the plurality deviate from each other no more than about +/−10%, preferably no more than about +/−5%, and most preferably no more than about +/−1% of a given quantitative measure of the parameter. As an example, the particles may be homogeneously porous. This means that the degree of porosity within the particles of the plurality differs by not more than +/−10% of the average porosity. In other instances, a plurality that is homogeneous means that all the particles in the plurality were treated or processed in the same manner, including for example exposure to the same agent regardless of whether every particle ultimately has all the same properties. In still other embodiments, a plurality that is homogeneous means that at least 80%, preferably at least 90%, and more preferably at least 95% of particles are identical for a given parameter.

The plurality of particles may be heterogeneous for one or more parameters or characteristics. A plurality that is heterogeneous for a given parameter, in some instances, means that particles within the plurality deviate from the average by more than about +/−10%, including more than about +/−20%. Heterogeneous particles may differ with respect to a number of parameters including their size or diameter, their shape, their composition, their surface charge, their degradation profile, whether and what type of agent is comprised by the particle, the location of such agent (e.g., on the surface or internally), the number of agents comprised by the particle, etc. The invention contemplates separate synthesis of various types of particles which are then combined in any one of a number of pre-determined ratios prior to contact with the sample. As an example, in one embodiment, the particles may be homogeneous with respect to shape (e.g., at least 95% are spherical in shape) but may be heterogeneous with respect to size, degradation profile and/or agent comprised therein.

Particle size, shape and release kinetics can also be controlled by adjusting the particle formation conditions. For example, particle formation conditions can be optimized to produce smaller or larger particles, or the overall incubation time or incubation temperature can be increased, resulting in particles which have prolonged release kinetics.

The particles may also be coated with one or more stabilizing substances, which may be particularly useful for long term depoting with parenteral administration or for oral delivery by allowing passage of the particles through the stomach or gut without dissolution. For example, particles intended for oral delivery may be stabilized with a coating of a substance such as mucin, a secretion containing mucopolysaccharides produced by the goblet cells of the intestine, the submaxillary glands, and other mucous glandular cells.

To enhance delivery the particles may be incorporated, for instance, into liposomes, virosomes, cationic lipids or other lipid based structures. The term “cationic lipid” refers to lipids which carry a net positive charge at physiological pH. Such lipids include, but are not limited to, DODAC, DOTMA, DDAB, DOTAP, DC-Chol and DMRIE. Additionally, a number of commercial preparations of cationic lipids are available. These include, for example, LIPOFECTIN® (commercially available cationic liposomes comprising DOTMA and DOPE, from GIBCO/BRL, Grand Island, N.Y., USA); LIPOFECTAMINE® (commercially available cationic liposomes comprising DOSPA and DOPE, from GIBCO/BRL); and TRANSFECTAM® (commercially available cationic lipids comprising DOGS in ethanol from Promega Corp., Madison, Wis., USA). A variety of methods are available for preparing liposomes e.g., U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, 4,946,787; and PCT Publication No. WO 91/17424. The particles may also be composed in whole or in part of GRAS components. i.e., ingredients are those that are Generally Regarded As Safe (GRAS) by the US FDA. GRAS components useful as particle material include non-degradable food based particles such as cellulose.

The carrier domain can serve several functions. As discussed above, it may be useful for targeting the product to a specific region, such as a tissue. In that instance it could include a targeting agent such as a glycoprotein, an antibody, or a binding protein.

Further, the size of the carrier domain may be adjusted based on the particular use of the pro-diagnostic reagent. For instance, the carrier domain may be designed to have a size greater than 5 nm. Particles, for instance, of greater than 5 nm are not capable of entering the urine, but rather, are cleared through the reticuloendothelial system (RES; liver, spleen, and lymph nodes). By being excluded from the removal through the kidneys any uncleaved pro-diagnostic reagent will not be detected in the urine during the analysis step. Additionally, larger particles can be useful for maintaining the particle in the blood or in a tumor site where large particles are more easily shuttled through the vasculature. In some embodiments the carrier domain is 500 microns-5 nm, 250 microns-5 nm, 100 microns-5 nm, 10 microns-5 nm, 1 micron-5 nm, 100 nm-5 nm, 100 nm-10 nm, 50 nm-10 nm or any integer size range there between. In other instances the carrier domain is smaller than 5 nm in size. In such instance the nanoparticle will be cleared into the urine. However, the presence of free detectable marker can still be detected for instance using mass spectrometry. In some embodiments the carrier domain is 1-5 nm, 2-5 nm, 3-5 nm, or 4-5 nm.

Optionally the carrier domain may include a biological agent. In one embodiment a biological agent could be incorporated in the carrier domain or it may make up the carrier domain. For instance, it may form the scaffold or platform that the proteolytic domain is attached to. Thus the compositions of the invention can achieve two purposes at the same time, the diagnostic methods and delivery of a therapeutic agent. In some embodiments the biological agent may be an enzyme inhibitor. In that instance the biological agent can inhibit proteolytic activity at a local site and the detectable marker can be used to test the activity of that particular therapeutic at the site of action. HIV is an example of the disease in which active proteases can be monitored. In this embodiment the composition may include a micro-particle or other delivery device carrying a protease inhibitor. The protease susceptible site may be sensitive to the HIV proteases such that feedback can be provided regarding the activity of the particular protease inhibitor.

Enzyme Susceptible Domains

The enzyme susceptible domain is a portion of a pro-diagnostic reagent that is typically connected to a carrier domain. An enzyme susceptible domain may be directly (e.g., via a peptide bond) or indirectly (e.g., by a linker) connected to a carrier domain. An enzyme susceptible domain, as used herein, is the portion of the modular structure (e.g., a pro-diagnostic reagent) that promotes the enzymatic reaction in a subject or tissue sample, causing the release of a detectable marker (e.g., a signature molecule).

The enzyme susceptible site is dependent on enzymes that are active in a specific disease state. For instance, tumors are associated with a specific set of enzymes. If the disease state being analyzed is a tumor then the product is designed with an enzyme susceptible site that matches that of the enzyme expressed by the tumor or other diseased tissue. Alternatively, the enzyme specific site may be associated with enzymes that are ordinarily present but are absent in a particular disease state. In this example, a disease state would be associated with a lack or signal associated with the enzyme, or reduced levels of signal compared to a normal reference. An enzyme, as used herein refers to any of numerous proteins produced in living cells that accelerate or catalyze the metabolic processes of an organism. Enzymes act on substrates. The substrate binds to the enzyme at a location called the active site just before the reaction catalyzed by the enzyme takes place. Enzymes include but are not limited to proteases, glycosidases, lipases, heparinases, phosphatases.

In some embodiments, an enzyme susceptible detectable domain comprises a substrate for a protease (e.g., an amino acid sequence that is cleaved by a protease). In some embodiments, the protease substrate is a substrate of a disease-associated enzyme. Examples of enzymes that are associated with disease in a subject include serine proteases, cysteine proteases, threonine proteases, aspartic proteases, glutamic proteases, metalloproteases, etc. Examples of substrates for disease-associated enzymes include but are not limited to SLKRYGGG (SEQ ID NO: 3; plasma kallikrein), AAFRSRGA (SEQ ID NO: 4; kallikrein 1), xxFRFFxx (SEQ ID NO: 5; cathepsin B), QSVGFA (SEQ ID NO: 6; cathepsin B), LGLEGAD (SEQ ID NO: 7; cathepsin K), GPLD (SEQ ID NO: 8; subunit beta 1c), LGVLIV (SEQ ID NO: 9; cathepsin D), GLVLVA (SEQ ID NO: 10; cathepsin E), PAALVG (SEQ ID NO: 11; MMP2), GPAGLAG (SEQ ID NO: 12; MMP9), GGPLGVRGKK (SEQ ID NO: 13; MMP9), and GGfPRSGGGK (f=d-stereoisomer of phenylalanine; SEQ ID NO: 14; thrombin).

The enzyme susceptible site may be optimized to provide both high catalytic activity (or other enzymatic activity) for specified target enzymes but to also release optimized detectable markers for detection. Patient outcome depends on the phenotype of individual diseases at the molecular level, and this is often reflected in expression of enzymes. The recent explosion of bioinformatics has facilitated exploration of complex patterns of gene expression in human tissues (Fodor, S. A. Massively parallel genomics. Science 277, 393-395 (1997)). Sophisticated computer algorithms have been recently developed capable of molecular diagnosis of tumors using the immense data sets generated by expression profiling (Khan J, Wei J S, Ringner M, Saal L H, Ladanyi M, Westermann F, et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 2001; 7:673-679.). This information can be accessed in order to identify enzymes and substrates associated with specific diseases. Based on this information the skilled artisan can identify appropriate enzyme or substrates to incorporate into the pro-diagnostic reagent.

Table 1 provides a non-limiting list of enzymes associated with (either increased or decreased with respect to normal) disease and in some instances, the specific substrate. Table 2 provides a non-limiting list of substrates associated with disease or other conditions. Numerous other enzyme/substrate combinations associated with specific diseases or conditions are known to the skilled artisan and are useful according to the invention.

TABLE 1 Disease Enzyme Substrate Cancer MMP collagens, gelatin, various ECM proteins Cancer MMP-2 type IV collagen and gelatin Cancer MMP-9 type IV and V collagens and gelatin Cancer kallikreins kininogens, plasminogen Cancer cathepsins broad spectrum of substrates Cancer plasminogen activator, tPA Plasminogen Cancer ADAM (A Diseintegrin And various extracellular domains Metalloprotease, also MDC, of transmembrane proteins Adamalysin) Pancreatic carcinoma MMP-7 various, e.g. collagen 18, FasL, HLE, DCN, IGFBP-3, MAG, plasminogen, other MMPs Pancreatic Cancer ADAM9, ADAM15 various extracellular domains of transmembrane proteins Prostate adenocarcinoma Matriptase, a type II unspecific, cleaves after Lys or transmembrane serine protease Arg residues Prostate cancer Kallikrein 3 kininogens, plasminogen Prostate cancer ADAM15 various extracellular domains of transmembrane proteins Ovarian carcinoma Kallikrein 6 kininogens, plasminogen Epithelial-derived tumors Matriptase, a type II unspecific, cleaves after Lys or (breast, prostate, ovarian, colon, transmembrane serine protease Arg residues oral) Ovarian Cancer MMP-2, MMP-9, kallikrein-10 type IV and V collagens and (hk-10) gelatin, kininogens, plasminogen Breast, gastric, prostate cancer cathepsins B, L and D broad spectrum of substrates Endometrial cancer cathepsin B unspecific cleavage of a broad spectrum of substrates without clear sequence specificity esophageal adenocarcinoma cathepsin B unspecific cleavage of a broad spectrum of substrates without clear sequence specificity Invasive cancers, metastases type II integral serine proteases (dipeptidyl peptidase IV (DPP4/CD26), seprase/fibroblast activation protein alpha (FAPalpha) and related type II transmembrane prolyl serine peptidases)) Invasive cancers, metastases Seprase various ECM proteins Viral Infections All Retroviruses viral protease precursor GagPol fusion HIV HIV protease (HIV PR, an precursor Gag and GagPol aspartic protease) proteins Hepatitis C NS3 serine protease viral precursor polyprotein Dengue Dengue protease autocleavage (NS2B/NS3), NS3/NS4A and NS4B/NS5 cleavage West Nile NS2B/NS3pro viral precursor polyprotein Bacterial Infections Legionella spp. zinc metalloprotease Me-Arg-Pro-Tyr Meninogencephalitis histolytic cysteine protease Streptococcus pyogenes (Group streptococcal pyrogenic exotoxin extracellular matrix, A Streptococcus) B (SpeB) immunoglobulins, complement components Clostridium difficile Cwp84 fibronectin, laminin, vitronectin and other ECM proteins Additional Diseases Alzheimer's disease BACE-1,2 (Alzheimer secretase) β-amyloid precursor protein Stroke and recovery MMP, tPA cardiovascular disease Angiotensin Converting Enzyme angiotensin I, bradykinin (ACE) Atherosclerosis cathepsin K, L, S broad spectrum of substrates arthritis MMP-1 triple-helical fibrillar collagens rheumatoid arthritis thrombin Osteopontin osteoarthritis thrombin Osteopontin osteoporosis/osteoarthritis cathepsin K, S broad spectrum of substrates Arthritis, inflammatory joint Aggrecanase (ADAMTS4, aggrecans (proteoglycans) disease ADAMTS11) thrombosis factor Xa (thrombokinase) Prothrombin thrombosis ADAMTS13 von Willebrand factor (vWF) thrombosis plasminogen activator, tPA Plasminogen Stress-induced Renal pressure Prostasin epithelial Na channel subunits natriuresis

TABLE 2 DISEASE TARGET SUBSTRATE ENZYME Inflammation Interleukin 1 beta MMP-2, MMP-3, MMP-9, Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Pituitary gland IGFBP-3 MMP-1, MMP-3, MMP-9, dysfunction, abnormal Trypsin, chymotrypsin, pepsin, bone density, growth Lys-C, Glu-C, Asp-N, Arg-C disorders Cancer TGF-beta MMP-9, Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cancer, autoimmune TNF MMP-7, Trypsin, chymotrypsin, disease pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cancer, autoimmune FASL MMP-7, Trypsin, chymotrypsin, disease pepsin, Lys-C, Glu-C, Asp-N, Arg-C Wound healing, cardiac HB-EGF MMP-3, Trypsin, chymotrypsin, disease pepsin, Lys-C, Glu-C, Asp-N, Arg-C Pfeiffer syndrome FGFR1 MMP-2, Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cancer Decorin MMP-2, MMP-3, MMP-7, Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cancer Tumor associated Endoglycosidases carbohydrate antigens Cancer Sialyl Lewis^(a) O-glycanase Cancer Sialyl Lewis^(X) O-glycanase Cancer/Rheumatoid VEGF Trypsin, chymotrypsin, pepsin, Arthritis, pulmonary Lys-C, Glu-C, Asp-N, Arg-C hypertension Cancer EGF Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cancer IL2 Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cancer IL6 Trypsin, chymotrypsin, pepsin, inflammation/angiogenesis Lys-C, Glu-C, Asp-N, Arg-C Cancer IFN-γ Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cancer TNF-α Trypsin, chymotrypsin, pepsin, inflammation/angiogenesis, Lys-C, Glu-C, Asp-N, Arg-C Rheumatoid Arthritis Cancer, Pulmonary TGF-β Trypsin, chymotrypsin, pepsin, fibrosis, Asthma Lys-C, Glu-C, Asp-N, Arg-C Cancer, Pulmonary PDGF Trypsin, chymotrypsin, pepsin, hypertension Lys-C, Glu-C, Asp-N, Arg-C Cancer, pulmonary Fibroblast growth factor Trypsin, chymotrypsin, pepsin, cystadenoma (FGF) Lys-C, Glu-C, Asp-N, Arg-C Cancer Brain-derived neurotrophic Trypsin, chymotrypsin, pepsin, factor (BDNF) Lys-C, Glu-C, Asp-N, Arg-C Cancer Interferon regulatory Trypsin, chymotrypsin, pepsin, factors (IRF-1, IRF-2) Lys-C, Glu-C, Asp-N, Arg-C Inhibitor of tumor MIF Trypsin, chymotrypsin, pepsin, suppressors Lys-C, Glu-C, Asp-N, Arg-C Lymphomas/carcinomas, GM-CSF Trypsin, chymotrypsin, pepsin, alveolar proteinosis Lys-C, Glu-C, Asp-N, Arg-C Cancer invasion M-CSF Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Chemical carcinogenesis, IL-12 Trypsin, chymotrypsin, pepsin, multiple sclerosis, Lys-C, Glu-C, Asp-N, Arg-C rheumatoid arthritis, Crohn's disease Natural Killer T cell IL-15 Trypsin, chymotrypsin, pepsin, leukemias, inflammatory Lys-C, Glu-C, Asp-N, Arg-C bowel disease, rheumatoid arthritis Cirrhosis Tissue inhibitor of MMPs Trypsin, chymotrypsin, pepsin, (TIMPs) Lys-C, Glu-C, Asp-N, Arg-C Cirrhosis Collagen I, III MMP-1, MMP-8, Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C Cirrhosis Collagen IV, V MMP-2, Trypsin, chymotrypsin, pepsin, Lys-C, Glu-C, Asp-N, Arg-C

In some embodiments, the enzyme susceptible domain is a cancer-specific (e.g., tumor-specific) enzyme susceptible domain. As used herein, “cancer-specific enzyme susceptible domain” refers to an enzyme susceptible domain that is capable of being cleaved by a protease that is present (or upregulated) in a subject having a cancer (e.g., a malignant tumor, metastatic cancer, etc.). For example, certain cancers (e.g. metastatic cancers) are associated with upregulation of specific enzymes (e.g. ADAM28, MMP9, MMP12, ACE, C2, ADAMTS5, HTRA4, MMP16, MMP1, MMP3, MMP4, MMP7, MMP8, Cathepsin B, Cathepsin L, Cathepsin S, ADAM10, ADAM12, PRSS3, uPA, etc.).

The enzyme susceptible detectable marker is preferably a polymer made up of a plurality of chemical units. A “chemical unit” as used herein is a building block or monomer which may be linked directly or indirectly to other building blocks or monomers to form a polymer.

Linker Molecules

An enzyme susceptible detectable marker may be attached directly to the carrier. For instance it may be coated directly on the surface of microparticles using known techniques. Alternatively if the carrier is a protein material it may be directly connected through a peptide bond. Additionally, the enzyme susceptible detectable marker may be connected to the carrier domain through the use of a linker. As used herein “linked” or “linkage” means two entities are bound to one another by any physicochemical means. Any linkage known to those of ordinary skill in the art, covalent or non-covalent, is embraced. Thus, in some embodiments the carrier has a linker attached to an external surface, which can be used to link the enzyme susceptible detectable marker. Another molecule can also be attached to the linker. In some embodiments, two molecules are linked using a transpeptidase, for example Sortase A.

Aspects of the disclosure relate to the surprising discovery that the sensitivity and specificity of a pro-diagnostic reagent may be significantly improved by modulating presentation of the enzyme susceptible domain to its cognate enzyme, for example by varying the distance between the carrier domain and the enzyme susceptible domain of the pro-diagnostic reagent. For example, in some embodiments, a polymer comprising one or more linking molecules is used to adjust the distance between a carrier domain and an enzyme susceptible domain, thereby improving presentation of the enzyme susceptible domain to an enzyme.

In some embodiments, the distance between a carrier domain and an enzyme susceptible domain ranges from about 1.5 angstroms to about 1000 angstroms. In some embodiments, the distance between a carrier domain and an enzyme susceptible domain ranges from about 10 angstroms to about 500 angstroms (e.g., any integer between 10 and 500). In some embodiments, the distance between a carrier domain and an enzyme susceptible domain ranges from about 50 angstroms to about 800 angstroms (e.g., any integer between 50 and 800). In some embodiments, the distance between a carrier domain and an enzyme susceptible domain ranges from about 600 angstroms to about 1000 angstroms (e.g., any integer between 600 and 1000). In some embodiments, the distance between a carrier domain and an enzyme susceptible domain is greater than 1000 angstroms.

Examples of linking molecules include but are not limited to poly(ethylene glycol), peptide linkers, N-(2-Hydroxypropyl) methacrylamide linkers, elastin-like polymer linkers, and other polymeric linkages. Generally, a linking molecule is a polymer and may comprise between about 2 and 200 (e.g., any integer between 2 and 200, inclusive) molecules. In some embodiments, a linking molecule comprises one or more poly(ethylene glycol) (PEG) molecules. In some embodiments, a linking molecule comprises between 2 and 200 (e.g., any integer between 2 and 200, inclusive) PEG molecules. In some embodiments, a linking molecule comprises between 2 and 20 PEG molecules. In some embodiments, a linking molecule comprises between 5 and 15 PEG molecules. In some embodiments, a linking molecule comprises between 5 and 25 PEG molecules. In some embodiments, a linking molecule comprises between 10 and 40 PEG molecules. In some embodiments, a linking molecule comprises between 25 and 50 PEG molecules. In some embodiments, a linking molecule comprises between 100 and 200 PEG molecules.

Signature Molecules

The signature molecule is capable of being released from the pro-diagnostic reagent when exposed to an enzyme in vivo or in vitro. In some embodiments, the detectable marker (e.g., signature molecule) once released is free to travel to a remote site for detection. A remote site is used herein to refer to a site in the body that is distinct from the bodily tissue housing the enzyme where the enzymatic reaction occurs. In some embodiments, the bodily tissue housing the enzyme where the enzymatic reaction occurs is a tumor. In some embodiments, a remote site is a biological sample that is non-invasively obtained from a subject, for example a urine sample, or a blood sample.

Modification of the enzyme susceptible domain by an enzyme in vivo, results in the production of a signature molecule (e.g., a detectable marker). Alternatively, when the enzyme susceptible detectable marker is an enzyme the enzyme cleaves an endogenous substrate producing a detectable marker from the endogenous substrate. In some embodiments, the detectable marker is composed of two ligands joined by a linker, as described above. The detectable marker may be comprised of, for instance one or more of a peptide, nucleic acid, small molecule, fluorophore/quencher, carbohydrate, particle, radiolabel, MRI-active compound, inorganic material, organic material, with encoded characteristics to facilitate optimal detection.

Aspects of the disclosure relate to the surprising discovery that pro-diagnostic reagents comprising a ligand that binds to a target tissue and certain signature molecules are useful for in situ localization of enzymatic activity in a tissue (e.g., a tissue sample). Without wishing to be bound by any particular theory, pro-diagnostic reagents described by the disclosure bind to a target tissue prior to proteolysis, as opposed to enabling tissue binding after proteolysis, thereby allowing detection of the signature molecule in situ and thus localization of enzymatic activity within a tissue (e.g., a tumor within a tissue sample). Accordingly, in some embodiments, a signature molecule does not travel to a site that is remote from the bodily tissue housing the enzyme where the enzymatic reaction occurs. In some embodiments, a signature molecule remains bound to a carrier domain (e.g. directly or indirectly) after cleavage of an enzyme susceptible domain. For example, in some embodiments, a signature molecule comprises a FRET pair (e.g., a fluorophore and a quencher) linked by an enzyme susceptible domain, configured such that cleavage of the enzyme susceptible domain results in release of the quencher molecule from the carrier domain and detection of the carrier domain-linked fluorophore.

The detectable markers of the present disclosure comprise a detection ligand. A detection ligand is a molecule that is capable of being detected by any of a variety of methods. In some embodiments, the detectable marker comprises a detection ligand and a capture ligand, wherein the detection ligand and the capture ligand are distinct. While a capture ligand and a detection ligand will be distinct from one another in a particular detectable marker, the class of molecules that make up capture and detection ligands overlap significantly. For instance, many molecules are capable of being captured and detected. In some instances these molecules may be detected by being captured or capturing a probe. The capture and detection ligand each independently may be one or more of the following: a protein, a peptide, a polysaccharide, a nucleic acid, a fluorescent molecule, or a small molecule, for example. In some embodiments the detection ligand or the capture ligand may be, but is not limited to, one of the following: Alexa488, TAMRA, DNP, fluorescein, Oregon Green, Texas Red, Dansyl, BODIPY, Alexa405, Cascade Blue, Lucifer Yellow, Nitrotyrosine, HA-tag, FLAG-tag, His-tag, Myc-tag, V5-tag, S-tag, biotin or streptavidin. In some embodiments, the capture ligand and a detection ligand are connected by a linker, for example as described in International Application Publication No. WO2014/197840, filed Jun. 6, 2014, the entire contents of which are incorporated herein by reference. The purpose of the linker is prevent steric hindrance between the two ligands. Thus, the linker may be any type of molecule that achieves this. The linker may be, for instance, a polymer such as PEG, a protein, a peptide, a polysaccharide, a nucleic acid, or a small molecule. In some embodiments the linker is a protein of 10-100 amino acids in length. In other embodiments the linker is GluFib. Optionally, the linker may be 8 nm-100 nm, 6 nm-100 nm, 8 nm-80 nm, 10 nm-100 nm, 13 nm-100 nm, 15 nm-50 nm, or 10 nm-50 nm in length.

In some embodiments, a signature molecule is a mass encoded reporter, for example an iCORE as described in WO2012/125808, filed Mar. 3, 2012, the entire contents of which are incorporated herein by reference. Upon arrival in the diseased microenvironment, the iCORE agents interface with aberrantly active proteases to direct the cleavage and release of surface-conjugated, mass-encoded peptide substrates into host urine for detection by mass spectrometry (MS) as synthetic biomarkers of disease.

The signature molecule may be detected by any known detection methods to achieve the capture/detection step. A variety of methods may be used, depending on the nature of the detectable marker. Detectable markers may be directly detected, following capture, through optical density, radioactive emissions, nonradiative energy transfers, or detectable markers may be indirectly detected with antibody conjugates, affinity columns, streptavidin-biotin conjugates, PCR analysis, DNA microarray, and fluorescence analysis.

The capture assay in some embodiments involves a detection step selected from the group consisting of an ELISA, including fluorescent, colorimetric, bioluminescent and chemiluminescent ELISAs, a paper test strip or Lateral flow assay (LFA), bead-based fluorescent assay, and label-free detection, such as surface plasmon resonance (SPR). The capture assay may involve, for instance, binding of the capture ligand to an affinity agent.

The analysis step may be performed directly on the biological sample or the signature component may be purified to some degree first. For instance, a purification step may involve isolating the detectable marker from other components in the biological sample. Purification steps include methods such as affinity chromatography. As used herein an “isolated molecule” or “purified molecule” is a detectable marker that is isolated to some extent from its natural environment. The isolated or purified molecule need not be 100% pure or even substantially pure prior to analysis.

The methods for analysing detectable markers by identifying the presence of a detectable marker may be used to provide a qualitative assessment of the molecule (e.g., whether the detectable marker is present or absent) or a quantitative assessment (e.g., the amount of detectable marker present to indicate a comparative activity level of the enzymes. The quantitative value may be calculated by any means, such as, by determining the percent relative amount of each fraction present in the sample. Methods for making these types of calculations are known in the art.

The detectable marker may be labeled. For example, a label may be added directly to a nucleic acid when the isolated detectable marker is subjected to PCR. For instance, a PCR reaction performed using labeled primers or labeled nucleotides will produce a labeled product. Labeled nucleotides (e.g., fluorescein-labeled CTP) are commercially available. Methods for attaching labels to nucleic acids are well known to those of ordinary skill in the art and, in addition to the PCR method, include, for example, nick translation and end-labeling.

Labels suitable for use in the methods of the present invention include any type of label detectable by standard means, including spectroscopic, photochemical, biochemical, electrical, optical, or chemical methods. Preferred types of labels include fluorescent labels such as fluorescein. A fluorescent label is a compound comprising at least one fluorophore. Commercially available fluorescent labels include, for example, fluorescein phosphoramidides such as fluoreprime (Pharmacia, Piscataway, N.J.), fluoredite (Millipore, Bedford, Mass.), FAM (ABI, Foster City, Calif.), rhodamine, polymethadine dye derivative, phosphores, Texas red, green fluorescent protein, CY3, and CY5. Polynucleotides can be labeled with one or more spectrally distinct fluorescent labels. “Spectrally distinct” fluorescent labels are labels which can be distinguished from one another based on one or more of their characteristic absorption spectra, emission spectra, fluorescent lifetimes, or the like. Spectrally distinct fluorescent labels have the advantage that they may be used in combination (“multiplexed”). Radionuclides such as 3H, 1251, 35S, 14C, or 32P are also useful labels according to the methods of the invention. A plurality of radioactively distinguishable radionuclides can be used. Such radionuclides can be distinguished, for example, based on the type of radiation (e.g. α, β, or δ radiation) emitted by the radionuclides. The 32P signal can be detected using a phosphoimager, which currently has a resolution of approximately 50 microns. Other known techniques, such as chemiluminescence or colormetric (enzymatic color reaction), can also be used.

Quencher compositions in which a “donor” fluorophore is joined to an “acceptor” chromophore by a short bridge that is the binding site for the enzyme may also be used. The signal of the donor fluorophore is quenched by the acceptor chromophore through a process believed to involve resonance energy transfer (RET), such as fluorescence resonance energy transfer (FRET). Cleavage of the peptide results in separation of the chromophore and fluorophore, removal of the quench, and generation of a subsequent signal measured from the donor fluorophore. Examples of FRET pairs include 5-Carboxyfluorescein (5-FAM) and CPQ2, FAM and DABCYL, Cy5 and QSY21, Cy3 and QSY7, etc.

The disease or condition assessed according to the methods of the invention is any disease or condition that is associated with an enzyme. For instance, cancer, cardiovascular disease, arthritis, viral, bacterial, parasitic or fungal infection, Alzheimer's disease emphysema, thrombosis, hemophilia, stroke, organ dysfunction, any inflammatory condition, vascular disease, parenchymal disease, or a pharmacologically-induced state are all known to be associated with enzymes. A pharmacologically-induced state is a condition in which enzyme inhibitors and other agents directly or indirectly affect enzyme activities. Thus each of the these can be assessed or monitored or studied according to methods of the disclosure.

Tumor-Penetrating Ligands

Aspects of the disclosure relate to the discovery that pro-diagnostic reagents comprising certain ligands that bind to a target tissue (e.g., tumor-penetrating ligands) significantly improve the specificity and sensitivity of the reagents.

As used herein, a “ligand capable of binding to a tissue”, or “capable of binding to a tissue sample” refers to a molecule that specifically binds to a target tissue. The ligand may be a peptide, protein (e.g., antibody), small molecule, nucleic acid (e.g., DNA, RNA, etc.), aptamer, etc. For example, in some embodiments a ligand is a peptide or protein that binds to a receptor on the surface of a particular cell type (e.g., a tumor cell). Examples of tissue targeting ligands include but are not limited to Lyp1, iRGD, anti-cancer antibodies (e.g., Trastuzumab, Pertuzumab, Brentuximab, Tositumomab, Ibritumomab, etc.) and fragments thereof, etc.

A “tumor-penetrating peptide” is a peptide that binds to a receptor expressed by a cancer cell and mediates internalization of a cargo molecule (e.g., a pro-diagnostic reagent) into the tumor tissue. In some embodiments, a tumor-penetrating peptide binds to a receptor involved in the active transport pathway of the cell (e.g., cancer cell), for example neuropilin 1 (NRP-1) or p32. Additional examples of receptors involved in the active transport pathway of cells (e.g., cancer cells) include but are not limited to neuropilin-2 (NRP-2), transferrin receptor, LDLR, etc.

Examples of tumor-penetrating peptides include but are not limited to LyP1 (CGNKRTRGC; SEQ ID NO: 1), iRGD (CRGDKGPDC; SEQ ID NO:2), TT1, iNGR, and others for example as disclosed in Ruoslahti et al. J. Cell Biol. 188:759-768 (2014). In some embodiments, a suite of tumor-penetrating ligands specific for a range of primary receptors is produced by incorporation of the C-end rule motif, K/RXXK/R, which triggers the active internalization pathway of tumor cells.

Methods to Spatially Profile Protease Activity in Tissue

Aspects of the disclosure relate to the surprising discovery that pro-diagnostic reagents comprising a ligand that binds to a target tissue, and certain signature molecules, are useful for in situ localization of enzymatic activity in a tissue (e.g., a tissue sample).

As used herein, a biological sample is a tissue sample (such as a blood sample, a hard tissue sample, a soft tissue sample, etc.), a urine sample, saliva sample, fecal sample, seminal fluid sample, cerebrospinal fluid sample, etc. In preferred embodiments, the biological sample is a tissue sample. The tissue sample may be obtained from any tissue of the subject, including brain, lymph node, breast, liver, pancreas, colon, liver, lung, blood, skin, ovary, prostate, kidney, or bladder. The tissue from which the biological sample is obtained may be healthy or diseased. In some embodiments, a tissue sample comprises tumor cells or a tumor.

A tissue sample for use in methods described by the disclosure may be unmodified (e.g., not treated with any fixative, preservative, cross-linking agent, etc.) or physically or chemically modified. Examples of fixatives include aldehydes (e.g., formaldehyde, formalin, gluteraldehyde, etc.), alcohols (e.g., ethanol, methanol, acetone, etc.), and oxidizing agents (e.g., osmium tetroxide, potassium dichromate, chromic acid, potassium permanganate, etc.). In some embodiments, a tissue sample is cryopreserved (e.g., frozen). In some embodiments, a tissue sample is embedded in paraffin.

Without wishing to be bound by any particular theory, pro-diagnostic reagents as described herein are capable of binding to a target tissue prior to enzymatic cleavage of the enzyme susceptible domain, thereby preventing the diffusion of substrate and/or detectable signature molecule away from the site of enzymatic activity in a biological sample, such as a tissue sample. Accordingly, in some embodiments, after binding of the pro-diagnostic reagent to a tissue sample and subsequent cleavage of the enzyme susceptible domain, the pro-diagnostic reagent and signature molecule remain bound to the tissue sample.

Binding of the pro-diagnostic reagent to a tissue sample may be mediated by a molecule that specifically recognizes (e.g., specifically binds to) a site, such as a receptor, on a tissue sample. In some embodiments, the pro-diagnostic reagent comprises a tumor-penetrating peptide that binds to a tissue sample. In some embodiments, the pro-diagnostic reagent comprises another ligand that binds specifically to a target tissue, for example, charged peptides that specifically interact with the tissue (such as poly-arginine), peptides that specifically interact with target tissue cell membranes, and ligands that react chemically with the tissue to form covalent linkages (e.g., through reactive thiols or amines to link the pro-diagnostic reagent to the tissue).

The modality used for detection of the signature molecule (e.g., a signature molecule bound to a tissue sample and a carrier domain) will depend upon the characteristics of the signature molecule itself. For example, in some embodiments, the signature molecule is a peptide antigen and the detection method is a capture-based assay, such as ELISA. In some embodiments, the signature molecule is a fluorophore (e.g., a FRET pair comprising a fluorophore) and the detection method is a fluorescence-based imaging assay. Additional appropriate signature molecules and methods of detecting the same are described elsewhere in the disclosure and will be readily apparent to the skilled artisan.

Methods for Detecting Tumors in a Subject

In some aspects, the disclosure provides methods for detecting tumors in a subject. As used herein, a subject is a human, non-human primate, cow, horse, pig, sheep, goat, dog, cat, or rodent. In all embodiments human subjects are preferred. In aspects of the invention pertaining to cancer diagnosis in general the subject preferably is a human suspected of having cancer, or a human having been previously diagnosed as having cancer. Methods for identifying subjects suspected of having cancer may include physical examination, subject's family medical history, subject's medical history, biopsy, or a number of imaging technologies such as ultrasonography, computed tomography, magnetic resonance imaging, magnetic resonance spectroscopy, or positron emission tomography.

The disclosure is based, in part, on the discovery that pro-diagnostic reagents described herein are capable of detecting tumors smaller than 5 mm in diameter in a subject, which is surprising because generally the ability to identify cancer lesions with endogenous biomarkers was previously thought to be limited to detection of tumors greater than 1 cm in diameter. In some embodiments, methods described by the disclosure result in identification (e.g., detection) of a tumor smaller than 1 cm in a subject. In some embodiments, a tumor that is less than 1 cm, less than 0.5 cm, or less than 0.005 cm is detected using methods described by the disclosure. In some embodiments, the tumor that is detected is between 1 mm and 5 mm in diameter (e.g., about 1 mm, 2 mm, 3 mm, 4 mm, or about 5 mm) in diameter.

In some embodiments, the presence of a tumor in a subject is identified by obtaining a biological sample from a subject that has been administered a pro-diagnostic reagent as described by the disclosure and detecting the presence of a signature molecule in the biological sample. Generally, the biological sample may be a tissue sample (such as a blood sample, a hard tissue sample, a soft tissue sample, etc.), a urine sample, saliva sample, fecal sample, seminal fluid sample, cerebrospinal fluid sample, etc.

In some aspects, the disclosure relates to the discovery that pro-diagnostic reagents comprising certain modifications (e.g., surface presentation of enzyme susceptible domains, functionalization with a tumor-penetrating ligand, or a combination thereof) increase the sensitivity and selectivity of the pro-diagnostic reagent with regard to detection of the signature molecule at a site remote from the bodily tissue housing the enzyme where the enzymatic reaction occurs. Thus, in preferred embodiments, the biological sample is a sample that has been obtained non-invasively, for example a urine sample. In some embodiments, the biological sample is a blood sample.

The pro-diagnostic reagent, in some embodiments, comprises a modification that localizes the reagent to a target tissue (e.g., tissue of a tumor microenvironment). In some embodiments, the pro-diagnostic reagent comprises a tumor-penetrating peptide, for example a peptide that binds to a receptor involved in the active transport pathway of a cancer cell (e.g., p32 or NRP-1). Without wishing to be bound by any particular theory, a pro-diagnostic reagent comprising a tumor-penetrating peptide increases on-target (e.g., cell-type specific) and decreases off-target protease cleavage that occurs in vivo relative to a pro-diagnostic reagent that does not comprise a tumor-penetrating peptide.

Aspects of the disclosure are based on the observation that detection of a signature molecule in a urine signal increases when a primary receptor (e.g., a receptor expressed on the surface of a cancer cell) is matched with a tumor-penetrating ligand. For example, as described in the Examples section, administering a pro-diagnostic reagent comprising iRGD to a subject (e.g. a cell of a subject) having a tumor associated with expression of NRP-1 (the cognate receptor of iRGD) results in increased detection of signature molecules relative to administration of a pro-diagnostic reagent comprising iRGD to a subject (e.g. a cell of a subject) having a tumor that is not associated with expression of NRP-1. Accordingly, a cocktail of different tumor-penetrating peptides may be used, in some embodiments, to noninvasively and rapidly stratify patients on the basis of receptor expression. In some embodiments, methods described herein are useful as a companion diagnostic to monitor receptor status in tumors treated with precision medicines, such as integrin-targeted therapeutics.

Administration

Compositions described herein can be administered to any suitable subject. In some embodiments, pro-diagnostic reagents of the disclosure are administered to the subject in an effective amount for detecting enzyme activity. An “effective amount”, for instance, is an amount necessary or sufficient to cause release of a detectable level of detectable marker in the presence of an enzyme. The effective amount of a compound of the invention described herein may vary depending upon the specific compound used, the mode of delivery of the compound, and whether it is used alone or in combination. The effective amount for any particular application can also vary depending on such factors as the disease being assessed or treated, the particular compound being administered, the size of the subject, or the severity of the disease or condition as well as the detection method. One of ordinary skill in the art can empirically determine the effective amount of a particular molecule of the invention without necessitating undue experimentation. Combined with the teachings provided herein, by choosing among the various active compounds and weighing factors such as potency, relative bioavailability, patient body weight, severity of adverse side-effects and preferred mode of administration, an effective regimen can be planned.

Pharmaceutical compositions of the present invention comprise an effective amount of one or more agents, dissolved or dispersed in a pharmaceutically acceptable carrier. The phrases “pharmaceutical or pharmacologically acceptable” refers to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, such as, for example, a human, as appropriate. Moreover, for animal (e.g., human) administration, it will be understood that preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biological Standards.

As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, such like materials and combinations thereof, as would be known to one of ordinary skill in the art (see, for example, Remington's Pharmaceutical Sciences (1990), incorporated herein by reference). Except insofar as any conventional carrier is incompatible with the active ingredient, its use in the therapeutic or pharmaceutical compositions is contemplated. The agent may comprise different types of carriers depending on whether it is to be administered in solid, liquid or aerosol form, and whether it need to be sterile for such routes of administration as injection.

Aspects of the disclosure relate to systemic administration of a pro-diagnostic reagent to a subject. In some embodiments, the systemic administration is injection, optionally subcutaneous injection. Preferably the material is injected into the body but could also be administered by other routes. For instance, the compounds of the present invention can be administered intravenously, intradermally, intraarterially, intralesionally, intratumorally, intracranially, intraarticularly, intraprostaticaly, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, intramuscularly, intraperitoneally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularally, orally, topically, locally, inhalation (e.g., aerosol inhalation), injection, infusion, continuous infusion, localized perfusion bathing target cells directly, via a catheter, via a lavage, in creams, in lipid compositions (e.g., liposomes), or by other method or any combination of the forgoing as would be known to one of ordinary skill in the art (see, for example, Remington's Pharmaceutical Sciences (1990), incorporated herein by reference).

Examples MMP9 is Upregulated Across Human Cancers

One embodiment of an Activity-based Nanosensor (ABN) was designed on the basis of a proteolytic target that is highly elevated across numerous human cancers and that has a fundamental biological role in tumor progression. Analysis of mRNA expression data from Oncomine and The Cancer Genome Atlas (TCGA) showed that matrix metalloproteinase 9 (MMP9) is significantly upregulated compared with healthy controls across many human cancer types (FIG. 1A), and this can be used to distinguish cancer from normal tissue, via construction of receiver operating characteristic (ROC) curves (median area under the curve (AUC)=0.81; FIG. 1B). Furthermore, MMP9 mRNA levels are consistent across all stages, indicating that it can be used for both early and late stage diagnosis (FIGS. 2A-2B). Using MMP9 as a disease marker may be a valuable means to distinguish aggressive cancers from indolent ones, as it is been observed to play a critical role in the angiogenic switch needed for access to host vasculature when tumors reach 1-2 mm in diameter. Therefore, in some embodiments, MMP9 activity measurements prospectively reflect disease progression, and do not merely detect a byproduct of tumor growth, as is the case with many existing blood biomarkers.

MMP9 immunohistochemical staining (blindly scored by a pathologist) was performed on a tumor tissue microarray (TMA). Data indicate that MMP9 protein levels were elevated across many human cancers (FIGS. 1C-1F and FIGS. 2B-2C). An ABN was produced as a probe for MMP9 activity in vivo and as a platform for further development, establishing design principles that could be applied to other tumor-specific proteases found to be upregulated in cancer. Existing point-of-care technologies inadequately assess MMP9, as it acts locally at the tumor site and thus, typically cannot be assayed from body fluids with high sensitivity and specificity. Further exploration into other MMPs in breast cancer samples from TCGA revealed several other biomarker candidates that had elevated mRNA levels (FIG. 2D). These proteases could be assayed with multiplexed substrates in other embodiments of ABNs.

ABN Optimization Achieves Magnitude Fold Improvement

This example describes two strategies to engineer ABNs that were developed: (1) presentation of peptide substrates on the nanoparticle surface for maximal on-target and minimal off-target protease cleavage, and (2) modification of ABNs with tumor-penetrating ligands that engage active tumor trafficking pathways initiated by receptor binding. The strategies were also combined in order to increase cancer-specific signal generation.

In some embodiments, surface presentation of peptide substrates allows tuning of specificity between on- and off-target proteolytic cleavage rates of the substrate (e.g., MMP9 substrate). The cleavage kinetics of an MMP9 peptide substrate (PLGVRGK; SEQ ID NO: 15), flanked by a fluorescence resonance energy transfer (FRET) pair, at varying distances from the nanoparticle core (FIG. 3A) were tested. For this substrate, the rate of cleavage by MMP9 increased with increasing presentation distance (tether length) for all the substrate concentrations tested (0.5, 1.0, 2.0, 4.0 and 6.0 μM); as an example, cleavage velocity (V) increased from 0.24 to 0.96 nM s⁻¹ at 6 μM (FIG. 3B). Unexpectedly, this phenomenon was not generalizable across enzymes. For example, cleavage rates by the serine protease, thrombin, decreased with increasing presentation distance when the same substrate was tested (e.g., V at 6 μM of substrate decreased from 0.29 to 0.01 nM s⁻¹; FIG. 3C). Nor was it generalizable across substrates. For example, thrombin cleavage of a thrombin-selective substrate (fPRSGGG; lower case letter indicates _(D)-stereoisomer of the amino acid residue; SEQ ID NO: 16) was optimally presented at an intermediate length (FIG. 4). Taken together, these data indicate that it is possible to significantly augment the signal-to-noise ratio of ABNs by tuning presentation on the nanoparticle surface (FIG. 3D). The presentation of the MMP9 substrate on the ABNs described in this example exploited the increased on-target and decreased off-target protease cleavage that occurs for long tether lengths.

Next, localization of MMP9 ABN for sampling the tumor microenvironment in a living organism was investigated. In some embodiments, the benefit of tissue-level localization is magnified when applied to an activity-based system (e.g., ABNs), due to the synergy of accumulation and enzymatic amplification effects. To this end, a unique class of peptide ligands that mediate active internalization and transport of nanomaterials past tumor stroma and into the tumor tissue were employed; they are referred to here as tumor-penetrating peptides. In some embodiments, tumor-penetrating peptides are identified by phage-display screening.

The dual strategy of tuning MMP9-substrate presentation and increasing tumor-tissue access were applied to ABNs. Briefly, ABNs were decorated with the cyclic tumor-penetrating peptide, LyP-1 (CGNKRTRGC; SEQ ID NO: 1), which increases penetration of a variety of nanomaterials deep into the tumor parenchyma by binding its cognate receptor, p32, and engaging a secondary receptor, neuropilin-1 (NRP-1), which triggers an active transport pathway.

An MDA-MB-435 subcutaneous flank xenograft was used as a model of an epithelial tumor. MDA-MB-435 tumors have elevated p3231 and MMP932 expression. Non-tumor-penetrating (NTP) and LyP-1 ABNs were matched for substrate valency (FIGS. 5A-5B) and were measured to have a ˜60 nm hydrodynamic diameter and a slightly negative surface potential (FIG. 5C). Visualization of their fluorescent cores three hours after administration revealed that the amount of ABN accumulation in the tumors was similar to that in organs (FIGS. 3E-3G); addition of LyP-1 moderately increased tumoral accumulation (by ˜20%) and resulted in slightly decreased off-target accumulation in organs, versus NTP ABNs (FIG. 3G).

A pharmacokinetic mathematical model was used as a tool to understand how modifications affect the performance of ABNs. The model comprises a set of five ordinary differential equations solved in three separate compartments (blood, tumor and bladder). The equations are derived from transport and biochemical governing equations (e.g., Fick's Law and Michaelis-Menten kinetics) with variables fit to experimental data. On the basis of the in vitro and in vivo experimental ABN data presented in this example (FIGS. 3A-3G), three parameters of the model were modified: tumor-protease-specific cleavage (k_(cat) ^(MMP9)), off-target cleavage (k_(cat) ^(blood)) and tumoral accumulation (k^(NP) _(tumor)) (cat, catalysis; NP, nanoparticle; FIG. 3H). When applied to tumors of moderate size (10 mm diameter), the model indicated cooperation between the three parameters: increases in detection signal were greater when parameters were input simultaneously compared with the sum of each parameter input individually (FIG. 3I, light shaded bar). The model indicated negligible enhancement of the detection signal to increased tumoral accumulation by itself. When the same analysis was applied to small tumors (5 mm diameter), similar trends were observed (FIG. 3J). The model indicated interactions between parameters to be greater for these smaller tumors, suggesting that multi-parameter tuning is important when engineering ABNs for detection of small tumors. Lastly, the benefit of improved accumulation when combined with the other two parameters was examined. This was assessed by measuring the difference in the detection signal when all three parameters were input versus when just the modified protease cleavage parameters were input (FIG. 3K).

Tumor-Penetrating ABNs Detect Sub-5 mm Diameter Tumors

The minimum size of tumors that could be detected using tumor-penetrating ABNs was investigated. A urinary test (e.g., measurement of peptide fragments in the urine 1 h after ABN administration) was performed at 1, 2 and 3 weeks after initial tumorigenesis of MDA-MB-435 xenografts (FIG. 6A). Measurement of ABN half-life in the blood and the free substrate clearance in the blood and urine indicated that the signal decayed rapidly, with half-lives being far shorter than the seven-day intervals between particle administrations (FIGS. 7A-7B). At the time of each weekly urine test, the total tumor volume per mouse was measured, as determined by caliper measurements (FIGS. 8A-8C). Non-penetrating ABNs with tuned MMP9 substrate presentation discriminated tumors that were ˜150 mm³ in volume (FIG. 6B)—these volumes are approximately threefold smaller than those achieved when the substrate was directly presented on the nanoparticle surface. Consistent with the in silico analysis that indicated multi-parameter tuning would have a greater effect at small tumor sizes (FIG. 3J), the addition of tumor-penetrating ligands reduced the detection size limit to between 20 and 50 mm³, corresponding to tumor diameters of 3.4-4.6 mm (FIG. 6C). ROC analysis for tumor volumes of ≥50 mm³ yielded an AUC of 0.83 for non-penetrating ABNs (FIG. 6D) compared with 0.95 for LyP-1 ABNs (FIG. 6E), indicating that LyP-1 increased the diagnostic power of the ABNs. Urine signals were also elevated when tracked over time (FIGS. 8D-8E). The tumor-penetrating ligands markedly improved the urinary detection limit, reducing it from 150 mm³ to 30 mm³, despite their relatively moderate effect (1.2-fold increase) on accumulation. In some embodiments, this unanticipated dramatic enhancement may be explained by biological phenomena such as cell- and tissue-level distribution. Taken together, the combination of tuning of substrate presentation and tumor-penetration improved the size limit for detectable tumors by over an order of magnitude (˜14-fold), compared with limits of ˜500 mm³ for previous technology without these modifications.

ABNs Outperform a Clinical Test in an Ovarian Cancer Model

Early detection of ovarian cancer could yield substantial improvements in patient prognosis. Due to inadequate detection methods, 80% of current cases are diagnosed after the tumor has spread past the ovary. In addition, 70% of ovarian cancer patients relapse after being treated according to the standard of care, and therefore would greatly benefit from point-of-care longitudinal monitoring for early indications of relapse.

The tumor-penetrating ABN platform was used to detect a low tumor burden in an orthotopic disseminated xenograft model of high-grade serous ovarian cancer. The mouse model was established by intraperitoneal implantation of the human cell line OVCAR-8 (FIG. 9A), which displays surface p3234 and NRP-1 (FIG. 9B), and secretes human epididymis protein (HE4) (FIGS. 10A-10C) and MMP9. It was observed that OVCAR-8 conditioned media can cleave the MMP9 substrate, and that this activity can be inhibited by the broad-spectrum matrix-metalloprotease inhibitor, marimistat (FIG. 10D). Growth of tumors was monitored by bioluminescence tracking of luciferized cells (FIGS. 10E-10F). When implanted into the peritoneal space of mice, OVCAR-8 cells form disseminated tumor nodules (timescale of weeks) and the mice eventually accumulate ascites (timescale of months)—two disease presentations that also occur in human ovarian cancer patients. Two weeks after initial tumorigenesis, mice showed no overt signs of illness and had an average total tumor burden of 36 mm³ with a median nodule diameter of <2 mm (FIG. 9C and FIG. 11). After intravenous ABN administration, resected tumors showed significant accumulation of nanoparticles (FIG. 9D-9E) and the total tumoral accumulation depended strongly on tumor size (FIG. 11A).

The ability of ABNs to: (1) detect low-burden ovarian cancer and (2) outperform a clinical blood biomarker were tested. Detection by ABNs was compared to the blood biomarker HE4, as OVCAR-8 cells produce relatively high levels of this protein, on a par with four other human ovarian cancer cell lines (FIGS. 10B-10C). At a total tumor burden of 36 mm³, the urinary signal from the ABNs was significantly elevated versus mice with no tumors (FIG. 9F). This threshold of sensitivity is critical, as clinically approved imaging modalities can typically only resolve individual tumor nodules greater than 5 mm in diameter. Additionally, it has been estimated that to decrease serous ovarian cancer mortality by 50% with an annual screen, a test would have to be sensitive to tumors of <5 mm. In contrast, the blood biomarker HE4 was not elevated to detectable levels at this time point and was only significantly elevated three weeks post-tumorigenesis, when the average total burden was 88 mm³ (FIG. 9F and FIGS. 11B-11C). A comparison of the two diagnostic systems' detection powers indicated that ABN performance at two weeks (ROC−AUC=0.99) exceeded that of HE4 at two weeks (ROC−AUC=0.51) and three weeks (ROC−AUC=0.93), with improvements in the true positive and true negative rates (FIG. 9G). It was confirmed that the tumor nodule retrieval methodology described in this example accounted for greater than 80% of the tumor burden by measuring luminescence pre- and post-resection (FIGS. 11D-11G). The tumor burden remaining can be attributed to uncollected macroscopic and microscopic lesions.

The difference in the tumor volumes detected via an enzyme-linked immunosorbent assay (ELISA) of serum HE4 and those detected using the tumor-penetrating ABNs was 2.4-fold. Typically, early stage human serous ovarian carcinomas have a doubling time of four months. Extrapolating the benefit seen in detection compared with HE4 and assuming a simple monoexponential growth model of human ovarian cancer (N_(T)(t)=N_(T,0)e^((ln 2/[DT])t), where N_(T) is the starting tumor size and DT is the doubling time), diagnosis could occur five months sooner for ABNs versus the blood biomarker. Improving diagnosis time by five months could significantly impact the prognosis of ovarian cancer patients, especially when it is considered that ovarian cancers spend an average of one year at stages III and IV before they become clinically apparent.

Ligand-Receptor Matching Improves ABN Urinary Signal

Receptor expression on tumors varies by tumor type and patient. In this example, another ABN was produced using the tumor-penetrating ligand, iRGD (CRGDKGPDC; SEQ ID NO: 2). This peptide engages the same active-internalization pathway as LyP-1, but binds to α_(v)β₃ or α_(v)β₅ integrin heterodimers as its primary receptor, which are ectopically overexpressed in a large subset of cancers (FIG. 12A). The tumor-targeting peptides iRGD and LyP-1 were bound to ABNs and administered to an immunocompetent mouse model of colorectal liver metastasis (CLM), induced via an intrasplenic injection of p32-negative, integrin-positive and NRP-1-positive MC-26 cells (FIG. 12B-12C and FIGS. 13A-13C). MC-26 cells are derived from a mouse colorectal cancer line and secrete MMP9, which can be detected in the tumor nodules as well as in the tumor-adjacent liver, but not in non-tumor-bearing liver lobes (FIG. 12D). The stoichiometries for substrate conjugation on iRGD ABNs were similar to those used on the LyP-1 ABNs (FIG. 14A). Mouse and human MMPs exhibit a high degree of homology, and it was confirmed that mouse MMP9 cleaves the ABN MMP9 substrate (SEQ ID NO: XX; FIG. 14B). A study of ABN clearance in immunocompetent BALB/c mice indicated that no signal was detectable after 24 h in the urine, 48 h in the blood and 7 d in the tissues (FIGS. 15A-15C). This was consistent in the model of orthotopic ovarian cancer (FIG. 15D). Furthermore, no signs of toxicity were observed via histopathological assessment of tissues 3 h, 24 h and 7 d after ABN administration, when compared with PBS-injected controls (FIG. 16).

The growth of individual liver metastases was measured by MRI and was well-correlated with the bioluminescence signal of luciferized MC-26 cells, allowing monitoring of total tumor burden via bioluminescence imaging (FIG. 12E and FIG. 17). Nanoparticle (e.g., ABN) localization after intravenous administration of iRGD or LyP-1 ABNs was examined, and no changes in overall peri- and intra-organ accumulation were observed (FIG. 18A), but increased penetration of iRGD ABNs into the tumor metastases compared with LyP-1 (FIG. 12F and FIGS. 18B-18C). Application of either LyP-1 or iRGD ABNs in the urinary test resulted in distinct increases in signal when applied to mice with CLM compared with healthy mice (FIG. 12G) and those that underwent sham surgeries (FIG. 19). Consistent with low p32 and high integrin surface expression on MC-26 tumors (FIG. 12C), iRGD ABNs exhibited significantly improved diagnostic performance with relative reporter concentration increases that were greater than those for LyP-1 ABNs (AUC=1.00 versus 0.86, respectively). The urine signal was also more positively correlated with overall burden for iRGD versus LyP-1 ABNs (FIG. 19B). Administration of LyP-1 ABNs to CLM mice resulted in relative reporter concentration increases similar to those for non-penetrating ABNs administered in the hind flank model (FIG. 8B), thereby indicating that the presence of the primary receptor enhances the urinary signal.

ABN Zymography Tool Evaluates Substrates in Human Tissues

Typically, the evaluation and localization of protease activity on synthetic peptide substrates in excised tissues has been challenging because substrates can diffuse away after proteolysis. To investigate ABN activity in ex vivo tissues, a FRET-pair flanked substrate configured to monitor cleavage with fluorescence imaging was used (FIG. 20A). Combining existing zymography techniques with the ABNs (referred to in this example as ABNz) allowed the mapping of protease activity to tissue localization. In some embodiments, the critical step enabling monitoring involved binding the nanoparticle to the tissue before proteolysis occurred, thereby enabling localization. When iRGD ABNz was applied to frozen liver metastasis sections from CLM mice, the signal was dependent on both MMP activity, which was reduced by pharmacological inhibition, and binding, which was reduced when divalent cations necessary for integrin receptor engagement were omitted (FIG. 20A).

iRGD ABNz were also applied to a frozen human CRC TMA that contained biopsies from tumors and normal adjacent tissue (FIG. 20B). The extent of signal co-localization for activated ABNz, integrin and MMP9 in the cells of each tissue core was blindly scored. The results indicated that ABNz responded differently to tumor tissue compared with normal adjacent tissue, with 9 of 20 tumor cores showing a high signal, compared with only 3 of the 20 normal cores (FIG. 20C). It was observed that the normal adjacent tissues were collected from CRC patients and may have had elevated protease levels compared with tissue from healthy patients. A closer examination of the tissue (FIG. 20D-20E) showed examples of ABNz activation co-localizing with integrin and MMP9 staining. The observation that ABN-based signal generation correlates with MMP9 and integrin expression supports the applicability of this platform to the detection of human cancers. Beyond this application, the ABN technology described by the disclosure could also be used as a tool to profile human tissues for spatial information on protease activity that could support the translation of other protease-sensitive technologies and therapeutics.

Materials and Methods MMP9 Expression Analysis

MMP9 expression data was queried from Oncomine and TCGA where transcriptomic data were available for both tumor and control samples. The following cancers were analyzed: Head and Neck (Ginos et al., Cancer Res 2004; 13 normal, 41 tumor), Lung (Bhattacharjee et al., PNAS 2001; 17 normal, 132 tumor), Breast (TCGA; 61 normal, 529 tumor), Glioblastoma (TCGA; 5 normal, 82 tumor), Colon (TCGA; 41 normal, 286 tumor), Ovarian (TCGA; 8 normal, 586 tumor), Prostate (Yu et al., J Clin Oncol 2004; 23 normal, 89 tumor), Liver (Roessler et al., Cancer Res 2010; 220 normal, 225 tumor), Melanoma (Riker et al., BMC Med Genomics; 5 normal, 82 tumor) and Pancreatic (Badea et al., Hepatogastroenterology 2008; 39 normal, 39 tumor). Expression in tumors was normalized to controls from each data set.

Tissue Microarray Staining and Scoring

A multiple-organ cancer and normal-tissue microarray was obtained from US Biomax (MC5003b). The microarray was stained with anti-MMP9 antibodies (Abcam; 1:1,000). Blind scoring of cores was performed by a pathologist.

Synthesis of Peptides and Nanoparticles

All peptides were commercially synthesized. For recombinant enzyme studies and ABNz, intramoleculary quenched peptides were used: MMP substrate, 5-FAM-GGPLGVRGKK(CPQ2)-PEG2-C (SEQ ID NO: 17); thrombin substrate, 5-FAM-GGfPRSGGGK(CPQ2)-PEG2-C (SEQ ID NO: 18); where 5-FAM is the 5-carboxyfluorescein fluorophore, CPQ2 is the quencher, PEG2 is the linker polyethylene glycol, and lower case letters indicate the _(D)-stereoisomer of the residue. In vivo protease-sensitive substrates were synthesized to contain a urinary reporter comprised of a protease-resistant _(D)-stereoisomer of glutamate-fibrinopeptide B with a near-infrared dye for urinary detection (biotin-CGPLGVRGKK(Cy7)eGvndneeGffsar; Cy7 is cyanine7; SEQ ID NO: 19). Targeting peptides were synthesized and cyclized: LyP1, C-K(5-FAM)-C6-CGNKRTRGC (SEQ ID NO: 20); iRGD, C-PEG2-CRGDKGPDC (SEQ ID NO: 21); where C6 is the 6-aminohexanoic acid linker, Cys2 and Cys3 bridge.

Iron-oxide nanoparticles were formed by reacting iron(III) chloride hexahydrate and iron(II) chloride tetrahydrate with dextran. These nanoparticles are biocompatible and safe, and were cleared from the animal within five days. Nanoparticles were aminated by reaction with ammonium hydroxide. Size measurements were performed by dynamic light scattering (Malvern Instruments Nano ZS90). For conjugation of peptides to NPs, the NPs were first reacted with NHS-VivoTag 680 (VT680, Perkin Elmer) and MAL-PEG(5k)-SVA (Laysan Bio) to introduce sulfhydryl reactive handles. Cysteine-terminated peptides were then reacted with the NPs and unreacted peptide was filtered using spin filters (molecular weight cut-off, 30 kDa; Millipore). For experiments to identify optimal PEG lengths, PEG of varying lengths was purchased (Thermo Fisher) and reacted in the same manner. Nanoparticles were stored in PBS at 4° C. or at −20° C. Valencies of peptide conjugation and concentrations were quantified by absorbance (Molecular Devices SpectraMax Plus). Typical valencies were ˜60 protease-cleavable peptides, ˜5 targeting peptides and ˜10 VT680s per nanoparticle.

In Vitro Recombinant Protease Assays

Nanoparticles coupled with intramolecularly quenched peptide substrates were reacted with recombinant proteases to identify cleavage velocities. NPs were mixed with 1% (w/v) BSA (Sigma) and incubated with recombinant proteases (MMP-9, Enzo Life Sciences; thrombin, Haematologic Technologies) in a final volume of 50 μl in enzyme-specific buffers (MMP9 buffer: 50 mM Tris, 150 mM NaCl, 5 mM CaCl₂, 1 μM ZnCl₂, pH 7.5; thrombin: PBS) in a 384-well plate for time-lapse fluorimetry to measure dequenching at 37° C. (SpectroMax Gemini EM microplate reader). Michaelis-Menten constants were determined by assessing initial cleavage velocities at different substrate concentrations (Prism 5.0, GraphPad). The final MMP-9 concentration was 100 nM and the final thrombin concentration was 7 nM.

Cell Culture

The MDA-MB-435 human cancer cell line and MC-26 mouse colon carcinoma cell line were cultured in Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. The OVCAR-8 human ovarian cancer cell line was cultured in Roswell Park Memorial Institute medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. All cell lines used in these studies were tested for mycoplasma.

Antibody Staining and Flow Cytometry

To confirm the expression of targetable integrins on the MC-26 cells, cells were collected with enzyme-free cell-dissociation buffer (Thermo Fisher). Cells were stained for α_(v) integrin (550024, BD Pharmingen; 1:100), NRP-1 (AF566, R&D Biosystems; 1:100), and p32 (AB 2991, Millipore; 1:100) at 4° C. for 1 h and then probed with secondary antibodies conjugated to fluorophores using standard protocols. Cells were analyzed by flow cytometry on a BD LSR II flow cytometer.

ELISA for Ovarian Cancer Blood Biomarkers

Secreted and cytoplasmic levels of HE4 were measured by ELISA, according to the manufacturer's protocol (R&D Systems). Cultured supernatant and lysed cells from five cell lines were diluted as needed. All measurements were normalized to the number of cells and the secretion time.

MDA-MB-435 Subcutaneous Xenograft Studies

To generate subcutaneous grafts, three- to four-week-old female NCr nude mice (Taconic) were injected bilaterally with 5×106 MDA-MB-435 cells per flank. Urine measurements were made prior to tumor inoculation by intravenously injecting either 0.5 μM LyP1 or NTP ABNs (by protease cleavable peptide) in 200 μl of PBS at weekly intervals after inoculation. After nanoparticle injection, mice were placed in custom housing with a 96-well plate base for urine collection. After 1 h, their bladders were voided to collect between 100-200 μl of urine. For analysis, urine was diluted between 10- and 25-fold in PBS. Reporter concentration was quantified by measurement of Cy7 fluorescence using a LI-COR Odyssey infrared imaging system (with reference to a ladder). Tumor sizes were measured using digital electronic calipers (Marathon Management) and their volume was calculated as 0.5×length×width², where length and width are the larger and smaller dimensions, respectively. Total tumor volume was defined as the sum of the tumor volume in each flank. Mice were binned on the basis of tumor sizes and the urine signal was quantified for these bins. ROC curves were generated using Prism.

For NP quantification and determination of the NP distribution in organs and tumors, mice were sacrificed 3 h after the NP injection, and the organs were removed and scanned in the LI-COR Odyssey. Fluorescence from the nanoparticle scaffold (VT680) and the peptide (Cy7) was quantified using the ImageJ software package (National Institutes of Health).

Pharmacokinetic Mathematical Model

A description and derivation of the model is provided in Kwong, G. A. et al., Mathematical framework for activity-based cancer biomarkers. Proc. Natl. Acad. Sci. USA (2015). The measured properties of ABNs were inputted by modifying the base case values from the previous model. From the data shown in FIG. 3A-3G, MMP9 cleavage was found to increase 4-fold for 6 μM of substrate and thrombin cleavage decreased 1-fold at the same substrate concentration. These numbers were inputted to change the base case values for _(kcat, tumor) and _(kcat, background) by the respective fold changes observed. Here, the change in thrombin cleavage was assumed to be abstracted to background proteolysis for simplicity. From the data shown in FIG. 3G, it can be seen that tumoral accumulation increased 1.2-fold. The permeability term _(knp) _(_) _(tumor) in the ordinary differential equation by the observed difference. The nanoparticle half-life was modified to match that of the tested ABNs. For the 10 mm tumor, the base case model tumor-enzyme concentration of 700 nM was used, and for the 5 mm tumor, a concentration of 7 nM was used, which is in the range observed for tumors of this size.

Ovarian Cancer Orthotopic Model Studies

To generate an orthotopic model of human ovarian cancer, three- to four-week-old female NCr nude mice were injected intraperitoneally with 2×106 OVCAR-8 cells expressing firefly luciferase. Tumor burden was measured via luminescence using an in vivo imaging system (IVIS, PerkinElmer). Each mouse was sacrificed and the tumors were retrieved from all organs in the peritoneal space. Tumors were collected on a glass slide and scanned on a LI-COR Odyssey with 169 μm resolution. Widths and lengths were measured with ImageJ and tumor volume was calculated as described above for subcutaneous tumors. The reported tumor volumes for each group are the average of ten mice. The size distribution of nodules recovered from each mouse is shown in FIG. 11C. Before tumor induction, urine measurements were performed by injecting mice with 0.5 μM LyP1 ABNs. Approximately 200 μl of blood was collected and spiked with EDTA to a final concentration of 5 mM, and the blood cells were pelleted. Plasma was stored at −20° C. prior to HE4 quantification. HE4 levels were measured using the HE4 quantikine ELISA kit.

Liver Metastasis Model Studies

Immunocompetent six- to eight-week-old female BALB/c mice were injected with 5×104 syngeneic MC-26 cells expressing firefly luciferase in the subsplenic capsule to allow cells to seed the liver. After 90 s, the spleen was removed to prevent splenic tumors. Tumor growth was monitored by luminescence and MRI. Before induction of liver metastases, urine measurements were made by injecting 0.5 μM iRGD or LyP-1 ABNs. Post-tumor inoculation urine measurements were performed when tumor luminescence reached an average of 1-1.5×107 photons s⁻¹ cm⁻² sr⁻¹.

Toxicity and Clearance Studies

All studies were completed in immunocompetent six- to eight-week-old female BALB/c mice. After administration of ABNs or free reporter, 10 μl of blood and urine were collected at the indicated time points for fluorescence measurements. For tissue clearance and histopathological examination, animals were sacrificed at the indicated time points and their organs were fixed in formalin. Organs were imaged for ABNs with the LI-COR Odyssey as described above, before being embedded in paraffin and then sectioned.

Histology

Immediately after necropsy, organs were fixed in formalin for 24 h and stored at 4° C., before being embedded in paraffin, sectioned and stained. OVCAR-8 tumor sections were stained with p32 (Genscript custom antibody; 1:100) and NRP-1 (AF3870, R&D Biosystems; 1:100). MC-26 tumor sections were stained with α_(v) integrin (AB1930, Millipore; 1:100), p32 (AB2991, Millipore; 1:100) and NRP-1 (AF566, R&D Biosystems; 1:100).

Application of ABNz

Livers from CLM mice were extracted and immediately embedded and frozen in optimal-cutting-temperature compound. Before application of ABNz, liver sections were air dried and fixed in cold acetone. Protease substrates were designed in a similar manner to the intramolecularly quenched probes used in the in vitro cleavage experiments, except that the fluorophore and quencher positions were reversed. A fresh frozen acetone-fixed human CRC TMA was purchased. After hydration in PBS and blocking in 2% BSA solution for 1 h at 4° C., ABNz was applied and the microarray was incubated for 3 h at 4° C. with, and without, divalent cations in the buffer to allow for binding but no cleavage. The slide was washed and the buffer was exchanged with MMP9 cleavage buffer and incubated at 37° C. overnight in a humidified box. For inhibited controls, 50 μM marimastat was added to the binding and cleavage buffers. Slides were stained with α_(v) integrin (327902, BioLegend; 1:100) and MMP9 (137867, Abcam ab; 1:500) followed by application of the appropriate secondary antibodies (Jackson Immunolabs). Slides were scanned on a Pannoramic 250 Optimum (PerkinElmer) and co-localization was scored blindly by an independent researcher.

Statistical Analyses

All statistical analyses were performed using GraphPad Prism 5.0 or MATLAB R2013b. Each set of data shown is representative of studies repeated in at least two independent experiments. The sample sizes used for animal experiments (n=7-10) were estimated using a power test with an expected effect size of 50-100% and a variance of 30-50%. No animals were excluded from the analyses. The investigators were not blinded to the groups and treatments during the experiments. For each animal experiment, groups were established before tumorigenesis and therefore no randomization was used in the allocation of groups. 

1. A pro-diagnostic reagent comprising: (a) a carrier domain linked to a signature producing domain, wherein the signature producing domain comprises an enzyme susceptible domain linked to a signature molecule, wherein the enzyme susceptible domain is susceptible to cleavage by a disease-associated enzyme, and, (b) one or more tumor-penetrating ligands, wherein each tumor-penetrating ligand is linked to the carrier domain. 2-3. (canceled)
 4. The pro-diagnostic reagent of claim 1, wherein the carrier domain is a nanoparticle, RGD peptide, protein, polymer, aptamer, or antibody.
 5. (canceled)
 6. The pro-diagnostic reagent of claim 1, wherein the carrier domain is linked to the signature producing domain by a linker molecule. 7-8. (canceled)
 9. The pro-diagnostic reagent of claim 1, wherein the enzyme susceptible domain is susceptible to cleavage by an enzyme associated with cancer, tissue injury or damage, cardiovascular disease, arthritis, viral, bacterial, parasitic or fungal infection, Alzheimer's disease emphysema, thrombosis, hemophilia, stroke, organ dysfunction, any inflammatory condition, vascular disease, parenchymal disease, or a pharmacologically-induced state.
 10. The pro-diagnostic reagent of claim 1, wherein the disease-associated enzyme is a serine protease, matrix metalloprotease (MMP), thrombin, kallikrein, matriptase, hepsin, cathepsin, plasminogen activator, or ADAM.
 11. The pro-diagnostic reagent of claim 1, wherein the signature molecule is a peptide, nucleic acid, small molecule, fluorophore, carbohydrate, particle, radiolabel, MRI-active compound, ligand encoded reporter, ligand encoded reporter, or isotope coded reporter molecule (iCORE).
 12. The pro-diagnostic reagent of claim 1, wherein the signature molecule comprises a fluorescence resonance energy transfer (FRET) pair, wherein the FRET pair comprises a fluorophore molecule and a quenching molecule, optionally wherein the fluorophore molecule and the quenching molecule flank the enzyme susceptible domain. 13-14. (canceled)
 15. The pro-diagnostic reagent of claim 12, wherein the FRET pair is 5-Carboxyfluorescein (5-FAM) and CPQ2.
 16. The pro-diagnostic reagent of claim 1, wherein each of the one or more tumor-penetrating ligands is a peptide, polypeptide, polymer, aptamer, or small molecule.
 17. The pro-diagnostic reagent of claim 16, wherein each of the one or more tumor-penetrating ligand specifically binds to a p32 receptor, neuropilin-1 (NRP1) receptor, α_(v)β₃ integrin receptor, α_(v)β₅ integrin receptor, folate receptor, transferrin receptor, Her2 receptor, or EGFR.
 18. The pro-diagnostic reagent of claim 16, wherein each of the one or more tumor-penetrating ligand is LyP-1 (CGNKRTRGC; SEQ ID NO: 1), iRGD (CRGDKGPDC; SEQ ID NO: 2), TT1, or iNGR.
 19. The pro-diagnostic reagent of claim 1, wherein each of the one or more tumor-penetrating ligands is linked to the carrier domain by a linker molecule. 20-21. (canceled)
 22. The pro-diagnostic reagent of claim 1, wherein the carrier domain comprises a plurality of enzyme susceptible domains, a plurality of ligands capable of binding to the tissue sample, or a combination thereof.
 23. A method for determining the location of disease-associated enzyme activity in a tissue sample, the method comprising: (a) contacting a tissue sample obtained from a subject with a pro-diagnostic reagent, wherein the pro-diagnostic reagent comprises: (i) a carrier domain linked to a signature producing domain, wherein the signature producing domain comprises an enzyme susceptible domain linked to a signature molecule, wherein the enzyme susceptible domain is susceptible to cleavage by a disease-associated enzyme, and, (ii) one or more ligands capable of binding to the tissue sample, wherein each ligand is linked to the carrier domain; wherein the one or more ligands bind the carrier domain to the biological sample prior to cleavage of the enzyme susceptible domain by the disease-associated enzyme; and, (b) subjecting the tissue sample to an analysis method in order to detect the presence of the signature molecule, wherein the presence of the signature molecule in the tissue sample is indicative of the location of disease-associated enzymatic activity within the tissue sample.
 24. (canceled)
 25. The method of claim 23, wherein the tissue sample is a flash-frozen tissue sample.
 26. The method of claim 23, wherein the tissue sample is obtained from the brain, lymph node, breast, liver, pancreas, colon, liver, lung, blood, skin, ovary, prostate, kidney, or bladder of the subject.
 27. The method of claim 23, wherein the tissue sample comprises cancer cells.
 28. The method of claim 23, wherein the disease-associated enzyme is associated with cancer, tissue injury or damage, cardiovascular disease, arthritis, viral, bacterial, parasitic or fungal infection, Alzheimer's disease emphysema, thrombosis, hemophilia, stroke, organ dysfunction, any inflammatory condition, vascular disease, parenchymal disease, or a pharmacologically-induced state.
 29. The method of claim 23, wherein the disease associated enzyme is a serine protease, matrix metalloprotease (MMP), thrombin, kallikrein, matriptase, hepsin, cathepsin, plasminogen activator, or ADAM. 30-36. (canceled)
 37. The method of claim 23, wherein the signature molecule is a peptide, nucleic acid, small molecule, fluorophore, carbohydrate, particle, radiolabel, MRI-active compound, ligand encoded reporter, ligand encoded reporter, or isotope coded reporter molecule (iCORE). 38-40. (canceled)
 41. The method of claim 23, wherein each of the one or more ligands is a peptide, polypeptide (e.g., antibody), polymer, aptamer, or small molecule.
 42. The method of claim 41, wherein each of the one or more ligands specifically binds to a p32 receptor, neuropilin-1 (NRP1) receptor, α_(v)β₃ integrin receptor, α_(v)β₅ integrin receptor, folate receptor, transferrin receptor, Her2 receptor, or EGFR.
 43. The method of claim 41, wherein each of the one or more ligands is LyP-1 (CGNKRTRGC; SEQ ID NO: 1), iRGD (CRGDKGPDC; SEQ ID NO: 2), TT1, or iNGR. 44-50. (canceled)
 51. A method for detecting a tumor in a subject, the method comprising (i) administering to a subject a pro-diagnostic reagent, wherein the pro-diagnostic reagent comprises (a) a carrier domain linked to a signature producing domain, wherein the signature producing domain comprises an enzyme susceptible domain linked to a signature molecule, wherein the enzyme susceptible domain is susceptible to cleavage by a cancer-associated enzyme, and, (b) one or more tumor-penetrating ligands, wherein each tumor-penetrating ligand is linked to the carrier domain; (ii) subjecting a biological sample from obtained from the subject to an analysis method in order to detect the presence of the signature molecule, wherein the presence of the signature molecule in the biological sample is indicative of the subject having a tumor. 52-53. (canceled)
 54. The method of claim 51, wherein the tumor is less than about 1 cm in diameter.
 55. (canceled)
 56. The method of claim 51, wherein the biological sample is a urine sample or a blood sample.
 57. The method of claim 51, wherein the cancer-associated enzyme is a serine protease, matrix metalloprotease (MMP), thrombin, kallikrein, matriptase, hepsin, cathepsin, plasminogen activator, or ADAM. 58-64. (canceled)
 65. The method of claim 51, wherein the signature molecule is a peptide, nucleic acid, small molecule, fluorophore (e.g., a fluorophore, or a fluorophore/quencher pair, such as a FRET pair), carbohydrate, particle, radiolabel, MRI-active compound, ligand encoded reporter, or isotope coded reporter molecule (iCORE). 66-68. (canceled)
 69. The method of claim 51, wherein each of the one or more tumor-penetrating ligands is a peptide, polypeptide, polymer, aptamer, or small molecule.
 70. The method of claim 69, wherein each of the one or more tumor-penetrating ligands specifically binds to a p32 receptor, neuropilin-1 (NRP1) receptor, α_(v)β₃ integrin receptor, α_(v)β₅ integrin receptor, folate receptor, transferrin receptor, Her2 receptor, or EGFR.
 71. The method of claim 69, wherein each of the one or more ligands is LyP-1 (CGNKRTRGC; SEQ ID NO: 1), iRGD (CRGDKGPDC; SEQ ID NO: 2), TT1, or iNGR. 72-78. (canceled) 